Hi everybody,

I have a VM (ESX) running Windows Server 2008 r2 SP1 with WSUS 3.0, MDT 2010 Update1, WDS, and some other applications (F-Secure 9 for Windows Servers), which is experiencing some strange issues. After some updates and restarts I found it this morning with all of its shortcuts missing, as well as Administrative Tools. I scrolled through the system log but can't really see anything related to the issue.

I managed to resolve the Deployment Workbench by repairing the MDT installation in the Programs and Features menu, but can't really say that's an acceptable solution.

Does anyone have any ideas to might be the cause of this issue?

/Pelle

• Edited by pelleswe Monday, July 04, 2011 2:12 PM

Hello,

did you enable all required features for RSAT with add features?

If you miss the AD tools like dsa.msc etc. you have ton install the AD DS tools from the add server role. This will NOT install AD.

Thanks for your reply,

I'm not too familiar with RSAT but I don't think that is the issue. I'm not using this server to remotely administer other machines or active directory.

I use remote desktop from my client, Win7 Ent, to connect to the MDT server, which is experiencing these issues. And as I mentioned it seems like it's only the shortcuts that are missing - not the actual files. Using the Server Manager I can reach the WSUS console as well as the WDS etc.. MDT 2010 however is installed seprately so that's why using the repair tool enables its shortcuts again.

The menu for Administrative Tools is entirely empty.

Hi,

 

According to your description, the issue occurs when you connect to the server via remote desktop. How about log on to the server directly? You can also try another user account. I noticed that you said “all of its shortcuts missing”, do you mean all the shortcuts on the Start Menu? What can you see on Start Menu now? Do you see any errors during logon or when using the system? Have you got all the available updates installed properly?

 

Please find Administrative Tools item under the Control Panel, click to open it. Is this folder empty? If so, please open %Systemroot%\system32, create shortcut of the programs, like dsa.msc, copy the shortcut to Administrative Tools folder under Control Panel.

 

Please also check the following registry:

 

HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders

HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders

 

Check if there is a value Common Administrative Tools, if so, it should be C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools. Assume Windows is installed on C: drive.

 

The issue also can be caused due to some third party programs, please check the results in Clean Boot mode as well. Refer to:

 

1. Click "Start", go to "Run", and type "msconfig" in the open box to start the System Configuration Utility.

2. Click the "Services" tab, check the "Hide All Microsoft Services" box and click Disable All (if it is not gray).

3. Click the "Startup" tab, click "Disable All" and click "OK".

4. Restart your computer. If the "System Configuration Utility" window appears, please check the box and click "OK".

 

What is the result in this mode?

 

Thanks.

Nina

Hi Nina, thanks for your reply.

It doesn't matter wether i connect with remote desktop, or the vsphere client console, nor does it matter which user account I'm logging in with.

It's actually not ALL shortcuts, but pretty much :).. Windows update is missing from the start menu.. The administrative tools folder is empty.. The MDT Workbench was gone except for it's start menu folder, and the same goes for WAIK. Some shortcuts are still there though - Accessories for example (edit: actually there's even a lot of shortcuts missing from accessories. The ones that are there is: cmd, notepad, run, explorer, ease of access and system tools...).

There is a registry key for administrative tools in Shell Folders, but not in User Shell Folders - is that allright, or is something missing here?

Looking at the non-microsoft services in msconfig, there's really nothing out of the ordinary. All of those services are running on all my other servers, so I doubt they would be causing any problems here.

The server is a pretty recent deployment, installed with the W2K8R2SP1 iso downloaded from MS. At this moment I'm suspecting there's an update that somehow isn't working too well with this specific configuration. I might be reinstalling the server and choose its updates more carefully, but I'd prefer not to, 'cause the server is working correctly otherwise.

Hi,

 

Thanks for your update. It is normal if we cannot find Common Administrative Tools under User Shell Folders, please confirm whether the value is correct under Shell Folders. Can you see the Windows Update shortcut under C:\ProgramData\Microsoft\Windows\Start Menu? Please try another user account, same result? Please also open %Systemroot%\system32, create shortcut of the programs, like dsa.msc, copy the shortcut to Administrative Tools folder under Control Panel, any progress? I see that you have checked non-Microsoft services via msconfig, it is still recommended to disable all these services as suggested.

 

Thanks.

Nina

Once again, thanks for the time and effort you're putting into this matter.

I've got most of the administrative tools shortcuts back again by copying them from another server, and it seems like they are staying in place still =).

No, the Windows Update shortcut is not to be find under C:\ProgramData\Microsoft\Windows\Start Menu. I did try with different user accounts with same result. What might this indicate?

The registry key for common administrative tools under shell folders has a value of "C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools", so that seems to be correct.

The reason I'm not too willing to disable the services is because most of them are anti-virus related. I did however disable all the non-microsoft and non-anti-virus services with no result.

Hi

 

Have you had any luck with this i have the exact same problem but I have Server 2008 not R2

All shortcuts just have disappeared from all users and all default locations

is there a way to fully reset the default windows profile folders

This has happened to me twice now on the same server, I run about 60 windows server 2008 and 2008 R2 servers with various applications and only this deployment server has the problem, so i think it is somthing to do with that

I have tried looking in the event viewer and also tried everything in this post including removing the non MS servcies and nothing seems to work

thanks for any help

Any luck?

 

I am having the same issue.

 

Thanks,

 

Chris

Also having the same problem: Start menu shortcuts are missing, Administrative tools is empty and I'm getting a "Location not available"-error message when trying to open Administrative tools from the Control panel:

Error message says: "C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools refers to a location that is unavailable. It could be on a hard drive on this computer, or on a network. Check to make sure that the disk is properly inserted, or that you are connected to the internet or your network, and then try again. If it still cannot be located, the information might have been moved to a different location."

When looking for the above mentioned folder I noticed that the folder C:\ProgramData\Microsoft\Windows only contains three folders: Caches, DeviceMetadataStore, and WER. No folder named Start Menu!

Any idea what's causing this?

I am also having the same problem described here. We use Windows 2008 Server R2 SP1 for WDS and Deployment Workbench. I never really guessed my "Server Manager.Ink" missing was a BIG problem for a week, until I went to try and figure out why this error occurs when I log into the local Admin. We don't have any other users that log into this machine, and I don't really want to try a new user when I already know it won't work based off of everyone else's comments here.

 

As people before me have stated. All our shortcuts are missing from their respected admin tools locations, but they are still in the C:\Windows.

 

I'm guessing a bad patch? I keep our server up-to-date as possible, but without installing features I don't need. Keep in mind... I didn't do anything.

 

Add/remove features/roles... etc..

Anybody??? 

Right click the start button select properties, select the customize button under the "start menu" tab, scroll to the bottom. under system administrative tool choose "Display on the all programs menu and the start menu".
Problem Fixed

• Proposed as answer by alexxman Thursday, September 29, 2011 3:33 PM

Right click the start button select properties, select the customize button under the "start menu" tab, scroll to the bottom. under system administrative tool choose "Display on the all programs menu and the start menu".
Problem Fixed

I guess nobody will say anything. I might start a new thread, because of this. 

Thanks, but problem isn't fixed at all.

It's true, that you can make the administrative tools appear via the "start menu", but it will be gone when you log on the next time. Most of our servers are virtualized under citrix xen. Also the setting "don't show this screen..." from the server manager doesn't have any effect - it reappears every time I log on. And no - we don't have mandatory profiles.

 

I have the same problem. It seems like the culprit is either WDS or MDT 2010. It's strange really because it just happened one day without doing anything. Also I cannot open Computer Management by right-clicking on Computer in the Start Menu (nothing happens) and the logoff process hangs on "Please wait for the Remote Desktop Configuration" for 10-15 seconds (even after local login).

OMG, we had the exact same issue last week. Read the fix below.

We have multiple Hyper-V Hosts, all identical with 2008 R2 Datacenter. However, one of the Hosts has the WDS Role + MDT 2010 installed.

You won't believe what happened in a production environment, when a users asked me to reboot one of the VM's... after opening the Hyper-V console, there were no VM's listed! When I restarted the vmms service, I got an error saying "could not find the file specified". WTF.

After examining the logs, in one of the Hyper-V Worker logs, I found an error that the InitialStore.xml file could not be found. First, I wanted to check the disk array using the HP ACU, but the shortcuts in the Start Menu were missing! Then I saw that the Administrative Tools menu was completely empty. Right click on "My Computer"-> Manage didn't work either, so... here we are... a production machine, completely unmanagable.

Oh, and one other thing: when I wanted to use Remote Desktop to this host using my Windows 7 machine, I got an error saying that NLA is required! Win7 has NLA support, but I was unable to logon. Thanks to iLO I was able to change the RDP settings to "less secure", and then I was able to connect using RDP again.

I started by examining the C:\ProgramData folder. This is where the InitialStore.xml file is stored, and indeed: it was missing, but it felt like A LOT of folders were missing in the ProgramData folder. I logged in on another Hyper-V Host, and compared the ProgramData folder. I was missing 7 folder in ProgramData root and about 12 folders in ProgramData\Microsoft!

My solution was to use WSB (Windows Server Backup) and restore the complete ProgramData folder to something like C:\ProgramDataRestore. This is about 30 MB, so you'll have all the missing files within seconds. I made a backup of the current ProgramData folder, and then simply copyed ALL files/folders from the restore folder to the ProgramData folder with NO OVERWRITE, just merge.

Log off -> Log on -> everything was fixed! Start Menu was ok, Administrative Tools are back, changed RDP settings to NLA and worked!, Started hyper-v vmms service and started, opened Hyper-V console and YES all VM's where there!

To make this fix permanent: first thing to do: move WDS and MDT 2010 to a VM, or a non-Hyper-V Host or whatever.

• Proposed as answer by MpDay Friday, January 20, 2012 9:14 AM
• Edited by MpDay Friday, January 20, 2012 9:17 AM

I have the same problem on a windows 2008 R2 server (a member server in a domain) after installing WDS and MDT 2012 beta 2.

If I login as a domain admin I see the folder

c:\program data\microsoft\start menu but I can't access it even though file permission indicate I should be able to access it

If I login as the server Administrator the "start menu" folder is not there at all

It is not under c:\program data\microsoft\windows either

It does not even show up under c:\users\administrator

I don't have a backup of the program data folder.  

 

OMG, we had the exact same issue last week. Read the fix below.

We have multiple Hyper-V Hosts, all identical with 2008 R2 Datacenter. However, one of the Hosts has the WDS Role + MDT 2010 installed.

You won't believe what happened in a production environment, when a users asked me to reboot one of the VM's... after opening the Hyper-V console, there were no VM's listed! When I restarted the vmms service, I got an error saying "could not find the file specified". WTF.

After examining the logs, in one of the Hyper-V Worker logs, I found an error that the InitialStore.xml file could not be found. First, I wanted to check the disk array using the HP ACU, but the shortcuts in the Start Menu were missing! Then I saw that the Administrative Tools menu was completely empty. Right click on "My Computer"-> Manage didn't work either, so... here we are... a production machine, completely unmanagable.

Oh, and one other thing: when I wanted to use Remote Desktop to this host using my Windows 7 machine, I got an error saying that NLA is required! Win7 has NLA support, but I was unable to logon. Thanks to iLO I was able to change the RDP settings to "less secure", and then I was able to connect using RDP again.

I started by examining the C:\ProgramData folder. This is where the InitialStore.xml file is stored, and indeed: it was missing, but it felt like A LOT of folders were missing in the ProgramData folder. I logged in on another Hyper-V Host, and compared the ProgramData folder. I was missing 7 folder in ProgramData root and about 12 folders in ProgramData\Microsoft!

My solution was to use WSB (Windows Server Backup) and restore the complete ProgramData folder to something like C:\ProgramDataRestore. This is about 30 MB, so you'll have all the missing files within seconds. I made a backup of the current ProgramData folder, and then simply copyed ALL files/folders from the restore folder to the ProgramData folder with NO OVERWRITE, just merge.

Log off -> Log on -> everything was fixed! Start Menu was ok, Administrative Tools are back, changed RDP settings to NLA and worked!, Started hyper-v vmms service and started, opened Hyper-V console and YES all VM's where there!

To make this fix permanent: first thing to do: move WDS and MDT 2010 to a VM, or a non-Hyper-V Host or whatever.

We have the same exact problem. We just opened a case with Microsoft. We have Windows 2008 R2 Standard. WDS + MDT 2010 and yes, Hyper-V host. It happens twice. First time, we remove/add hyper-v to correct (recreate initialstore.xml). Doing so, I lost all my Snapshots. The second time it happens (NOW), I can't afford losing my vm's snapshots. Does anyone here have a solution better than a backup from this directory (C:\ProgramData\Microsoft) ?.

Thanks

I just moved my WDS service to another server. I shall wait and see if it happen again.... BTW, Microsoft told me that they are working on that case but no ETA for an actual patch. /fail

• Proposed as answer by michel687 Friday, July 06, 2012 1:34 AM

Installed WDS last week. Having this issue after first reboot.

So they know theres an issue and they're building a patch yet they leave this crap up so people can hose their servers. Makes sense to me.

Hi All,

I have the same issue. Server 2008 R2 with MDT & WDS installed. It's a VM on ESXi 4.0. After the last lot of windows updates the start menu is missing. To resolve the issue did the following: 

1. Restored"C:\ProgramData\Microsoft\Windows\Start Menu" from a backup
2. Right clicked the start menu >properties > Start menu Tab> Customize> Click the "use default settings" button.

My start menu was restored and working but after a reboot it's missing again.  

Is there a patch I can roll back to resolve this issue? We have nearly 600 servers and this is the only one I've noticed this issue on so far, which makes me think it's a WDS or MDT patch.

Hi, we are also having the same issue. running MDT 2010 & WDS. this is the 2nd time now that its happened. it looks like it deletes the programdata folder. restoring it from a shadowcopy seems to get it back working normally.

Hi All,

I have the same issue. Server 2008 R2 with MDT & WDS installed. It's a VM on ESXi 4.0. After the last lot of windows updates the start menu is missing. To resolve the issue did the following: 

1. Restored"C:\ProgramData\Microsoft\Windows\Start Menu" from a backup
2. Right clicked the start menu >properties > Start menu Tab> Customize> Click the "use default settings" button.

My start menu was restored and working but after a reboot it's missing again.  

Is there a patch I can roll back to resolve this issue? We have nearly 600 servers and this is the only one I've noticed this issue on so far, which makes me think it's a WDS or MDT patch.

Same issue here.

WDS, MDT both installed on 2008 R2 VM on an ESXi 5.0 host.

running WDS, MDT on 2008R2 on ESXi4.0 and we too have this issue. this is a worry indeed! no word from MS as yet?

Add me to the list. I can still manage the computer. I just lost a crap load of shortcuts and all administrative tools shortcuts are missing.

righto.. after a pretty lengthy session with MS support online, a very helpful chap (Kevin) has found a fix and somewhat of an explanation.

the fix:

RDP to another R2 (non MDT) server and open the admin tools folder, and copy the admin tools folder to the MDT one

get the properties of all the shortcuts/icons.

ensure they (I did it via copy & paste) are the same targets. in server 2008 they point to executables, but in R2 they point to MSC files..

not sure what's caused it, and he said he'd pass it on to the development team, and what concerns me more is the fear of 'other' changes I've not yet experienced caused by the same situation.

my suspicion is that some MDT update is not sufficiently structured to detect the difference between R2 and the old 2008.

worth a try, but looks good for the few Icons I've changed so far.

I found that no matter what i did, after a reboot they were gone again.

I blocked windows updates from applying, restored it back before the updates and it's been fine since then

hmm.. well I just rebooted mine and they're still there.... and working

I also note that he was in HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders

but I'm not sure if/what he changed in there... I suspect he was just ensuring that "Common Administrative Tools" still pointed to "C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools"

• Edited by rocklander Thursday, May 10, 2012 8:09 PM

All,

My WDS&MDT2010SP1 server is running with real machine, I got the exactly same error. Meanwhile, there is only one item KB976902 on the installed update list.

I have tried logging in as local administrator, another domain admin user, but still cannot get Administrative menu back. Moreover, when I click the "Administrative Tools" on the control pannel list, it says "C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools refers to a location that is unavailable..."

I searched entire local drives, but no result shows "Windows Deployment Service" or "Microsoft Deployment Toolkit" shortcut.

Any one got solution?

deployment workbench shortcut:

"C:\Program Files\Microsoft Deployment Toolkit\Bin\DeploymentWorkbench.msc"

windows deployment (services) shortcut:

%windir%\system32\WdsMgmt.msc

windows system image manager shortcut:

"C:\Program Files\Windows AIK\Tools\Image Manager\ImgMgr.EXE"

hth

Also having this same issue.  I'm wondering if this is fixed with MDT 2012?  I am considering rebuilding the OS and going with MDT 2012 just to bypass this issue.

i found my issue was due to having the Beta Version of the MDT 2012

we regressed to 2011 and all is has been fine since

I built a test VM with the beta and after about 1 week of being fine the admin tools went again

Hi

This has just happened to me as well, has anyone came to a conclusion to this?

I'm using 2008r2 standard VM

VSXI 4.1

WDS

MDT 2012 update 1

Things started falling over pretty quickly, I received a snap in error whilst using deployment work bench then everything because very unresponsive so rebooted, after reboot received the Remote Desktop NLA error, so accessed it via VSphere and reduced RD NLA setting.  Now everything is extremely unresponsive and administrative tools is missing.

I don't particularly want to rebuild the server with finding a fix as i suspect it will just happen again

Thanks

I am also having the same exact issue, MDT 2010, WDS, 2008R2, installed on a real machine, not VM.  Has anyone had any luck with resolving this issue???

I am also having the same exact issue, MDT 2010, WDS, 2008R2, installed on a real machine, not VM.  Has anyone had any luck with resolving this issue???

yes.. as per my previous posts.

I am also having the same exact issue, MDT 2010, WDS, 2008R2, installed on a real machine, not VM.  Has anyone had any luck with resolving this issue???

yes.. as per my previous posts.

My entire start menu folder under ProgramData\Microsoft\Windows was gone so just copying over the folder in your post would not have fixed my issue.  While your solution may have worked for some it did not work for me.  I would also consider the fix in your comment as more of a bandaid and not an actual solution to the problem.  This issues seem to span the entire gambit of WDS/MDT 2010-2012 and it doesn't care if you are a vm or an rm.  I am looking for an MS fix because I cannot afford to have to rebuild/restore my deployment server every time I reboot.  If this issue has continued on into the new version of MDT then I need to look for another deployment solution.    

FWIW, I'm having the same problem.  Windows Server 2008 R2 with WDS and MDT 2012.  last night, logging out of the server (from an RDP session) hung on the "Please wait for the Terminal Services Configuration..." message and then when that finally cleared (perhaps 20 minutes) i tried to log back in and got the message about the server requiring Network Level Authentication.  then it seemed that the PXE boot image got corrupt because booting to PXE got only so far (no prompts) before just rebooting on its own.

In WDS, i deleted the boot image and re-imported it from MDT 2012s "Boot" folder.  That seemed to get PXE back working.

oh yeah, all my Administrative Tools are gone and all that stuff everyone above is talking about - but that's another day.  for now i just need my deployment.

Hey Microsoft - you working on this? :)

I am also having the same exact issue, MDT 2010, WDS, 2008R2, installed on a real machine, not VM.  Has anyone had any luck with resolving this issue???

yes.. as per my previous posts.

My entire start menu folder under ProgramData\Microsoft\Windows was gone so just copying over the folder in your post would not have fixed my issue.  While your solution may have worked for some it did not work for me.  I would also consider the fix in your comment as more of a bandaid and not an actual solution to the problem.  This issues seem to span the entire gambit of WDS/MDT 2010-2012 and it doesn't care if you are a vm or an rm.  I am looking for an MS fix because I cannot afford to have to rebuild/restore my deployment server every time I reboot.  If this issue has continued on into the new version of MDT then I need to look for another deployment solution.    

to be fair.. your initial statement didn't exactly say that did it...

"I am also having the same exact issue, MDT 2010, WDS, 2008R2, installed on a real machine, not VM.  Has anyone had any luck with resolving this issue???"

as for band-aid.. sure, that's what I thought, but it was the MS support rep who applied it so.. there it is.

Well this same issue just happened to our MDT Server.

MDT 2010
WDS
2008 R2
on VMWare ESXi 5.1
and a whole bunch of other stuff

I enabled some updates in WSUS - particularly looks like KB2546951 (SQL 2008 SP3) and KB2528583 (SQL 2008 R2 SP1) and when they installed over the weekend  - server rebooted - problems started.

Staff could no longer log on to the network as printers on this particular server could not be allocated during login (script froze). Removed printers from login script and staff could then login.

Tried to remote to server - NLA error!

Found this thread and consoled to server via vSphere and discovered the C:\ProgramData was not all there and admin tools were missing also. Started up a replica and restored all I could from the replica and rebooted.

This fixed most of the issues and I could re-enable printer allocation in the login script and it fixed a whole bunch of other applications running on the server that were also failing.

The NLA error still exists so I have turned this off on the server but it does raise a question as to what else isn't working on the server that I am yet unaware of?

Many thanks for the suggestions on this thread or I would have been lost finding that C:\ProgramData folder was the issue.

Well this same issue just happened to our MDT Server.

MDT 2010
WDS
2008 R2
on VMWare ESXi 5.1
and a whole bunch of other stuff

I enabled some updates in WSUS - particularly looks like KB2546951 (SQL 2008 SP3) and KB2528583 (SQL 2008 R2 SP1) and when they installed over the weekend  - server rebooted - problems started.

Staff could no longer log on to the network as printers on this particular server could not be allocated during login (script froze). Removed printers from login script and staff could then login.

Tried to remote to server - NLA error!

Found this thread and consoled to server via vSphere and discovered the C:\ProgramData was not all there and admin tools were missing also. Started up a replica and restored all I could from the replica and rebooted.

This fixed most of the issues and I could re-enable printer allocation in the login script and it fixed a whole bunch of other applications running on the server that were also failing.

The NLA error still exists so I have turned this off on the server but it does raise a question as to what else isn't working on the server that I am yet unaware of?

Many thanks for the suggestions on this thread or I would have been lost finding that C:\ProgramData folder was the issue.

In addition to this I have now fixed the NLA problem.

I identified 3 certificates (keys) in C:\ProgramData\Microsoft\Crypto\RSA\MachineKeys\ that has their permissions mashed by the updates to SQL server.

One certificate needed 'Network Service' user with ReadOnly applying and 2 certificates required 'IIS_ISRS' ReadOnly applying. I got these permisssions by examining the replica machine before the update applied.

Hopefully most of the problems should have gone now but it remains to be seen!

Hello,

We had a Server (DC) crash in which we recovered using WBADMIN recovery tool.  After the recovery, we lost many of the "Administrative Tools" menu icons such as Active Directory Users and Computers, Active Directory Sites and Services, Active Directory Domains and Trust, ADSI EDIT, DHCP, DNS.

We're running 2008r2 (our only DC).

Has anyone seen this before?  And if so, how would i restore?

Very Kind Regards

I've seen something similar working with Double-Take repositories but conceivably the problem could occur in any number of scenarios - particularly where there may be a backup copy of some system locations involved.

As part of tidying up a backup job I manually removed a number of repository folders from our target servers.  The folders included the system state from other machines including all the Windows junctions that are used to link to Documents and Settings etc. The junctions were from another machine but it looks as though they were still referring to the local path.

When you delete a junction in Explorer the target folder is left intact, however when the reclebin is emptied the target folder is removed!

So hopefully this will explain how the problem occurs - even if not exactly why in a given case...

Ridiculous answer - didn't you even read the thread fully? I can't believe you then had the cheek to propose your junk response as the solution.

LEGEND!

Thank you :D

I've had the same issue with Server 2008 R2, WDS and MDT 2012.  I seem to recall once a long time ago finding a forum thread that suggested that Sophos antivirus was eating these icons and that there was no known fix other than to restore the shortcuts (C:\ProgramData\Microsoft\Windows\Start Menu) from backup.

Anyone else running Sophos on the server having the problem?

I've had this problem with servers running ESET and Trend Micro so I don't think it is caused by AV.

Thanks, this fix worked for me. fired up a 2008 r2 VM (hosted on the server that has the problem).

went to C:\ProgramData\Microsoft\Windows\Start Menu\Programs and copied the folder onto a shared drive on the host and then copied the contents of the folder into C:\ProgramData\Microsoft\Windows\Start Menu\Programs of the problem server and it worked. Admin tools on the start menu was re-populated and likewise he link in control panel. 

I have yet to log off and back on again to see if it is a permanent fix.... will update.

This occurred after I did a windows update last night which at some point failed but all the servers roles.... AD domain controller, DHCP, dns etc are all working as normal. 

I'm going to try logging off and back on and also rebooting to see if the issue reoccurs.

Thanks rocklander (and Kevin)

righto.. after a pretty lengthy session with MS support online, a very helpful chap (Kevin) has found a fix and somewhat of an explanation.

the fix:

RDP to another R2 (non MDT) server and open the admin tools folder, and copy the admin tools folder to the MDT one

get the properties of all the shortcuts/icons.

ensure they (I did it via copy & paste) are the same targets. in server 2008 they point to executables, but in R2 they point to MSC files..

not sure what's caused it, and he said he'd pass it on to the development team, and what concerns me more is the fear of 'other' changes I've not yet experienced caused by the same situation.

my suspicion is that some MDT update is not sufficiently structured to detect the difference between R2 and the old 2008.

worth a try, but looks good for the few Icons I've changed so far.

Thanks, this fix worked for me. fired up a 2008 r2 VM (hosted on the server that has the problem).
went to C:\ProgramData\Microsoft\Windows\Start Menu\Programs and copied the folder onto a shared drive on the host and then copied the contents of the folder into C:\ProgramData\Microsoft\Windows\Start Menu\Programs of the problem server and it worked. admin tools folder in programs and its link on the start menu was re-populated and likewise the link in control panel. 

I've logged off and back on and rebooted and all good.

Note that this occurred after I did a windows update last night, some point some or all failed and it rolled back the updates. Thankfully all the servers roles are all working as normal.... AD domain controller, dhcp, dns, hyper-v, dlna etc. Its just my server at home and I'm running the most recent windows 10 preview release on a VM and it is looking good and even 'Project Spartan' looks interesting as does the 3D printing app.

anyway thanks rocklander (and Kevin).

• Edited by BishTing 16 hours 51 minutes ago