Now that our software updates are all downloading I created and deployed a patch job to two 2012 servers.   I monitored the progress in Deployments.   Both machines went from unknown to in progress to compliant.  yet when I view the ccmcache folder each machine they are empty.  after rebooting both servers no updates were installed.  I looked in the control panel and even ran a wmic command.   The last know updates were applied over 6 months ago.  

What would cause our ConfigMan console tool to report back that both servers are compliant yet nothing installed on either box?

Not a lot of information for us to go on here.

Do the updates no longer appear?  Do you know the KB for the updates?

What do you see in the UpdatesDeployment.log log file (C:\Windows\CCM\Logs)?

What about WindowsUpdate.log (C:\Windows)?

Hello and thank you.  The updates never appear on the target file servers.   Not even after a reboot.  the c:\windows\ccmcache is empty on both servers, no folders, no files.   is that were software updates are downloaded?

the update deployment.log looks like this:

Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_cd0139f5-252e-44e5-8b7c-2ce97a242af5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_9ece576d-3654-411c-96c2-8c9836c4f33f) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_86f54a7f-84a9-47ef-a43d-f92d07f2dc63) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_f91a8a27-a764-49c5-98cf-b9f74a4c06d5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_5be19bff-6329-4c96-b2b1-50115b6a6be5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_42cbf3e5-d62e-4f31-84ff-31d6fbb81b57) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_8f30d731-2bc6-429e-817c-5827affa645d) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_aab9837c-e996-4dee-a586-59764f6d17e9) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_9b8fe594-4c6d-4dc4-9ada-3b52d4ae5250) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_6c8c0ac4-f40b-4e4b-aa83-1694fe0dbec2) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_91bbe473-1802-4538-b33e-6c578838e8e9) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_089872fb-ec7e-432d-b05c-01c263407033) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_7da3d1db-7f8f-464a-8494-1c286d9ed7b5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_365bd977-94ff-4b2b-b8eb-332838e2b6a5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_5002aab9-ff08-402f-ab15-38057d6c0f2f) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_726b8d92-d183-4a25-9588-d45d0dc86e5f) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_6d155681-7172-4dd7-9341-46d42ec794f5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_84baf93f-3645-4ef2-887a-d1e5e883adc7) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_922de694-c7e6-42ac-8738-95f5a8e2390e) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_3cb2203c-9c20-4f9e-98e9-7d6794491b1e) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_4dd3058e-6f32-4be6-ac74-abfa56da5d6b) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_c75dcc33-f1f6-4027-8a6d-0389f8bcb940) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_ea54ca3c-ef08-4eac-ae0e-8755d8c04c4b) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_71006fae-50da-42d2-8912-7cedea760c67) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_46b2d49e-2d54-440f-8ee7-69d615709172) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_0033933d-74d2-45e7-b790-740b68f51a3e) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_575c8151-e204-42cc-9169-20d1858f91fc) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_c18321d3-dda1-4728-bc08-f512bf85c03e) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_26f2a58a-0490-42f9-8ecd-08a256322743) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_3a611bb4-c01e-4c88-a057-6ac1a87a7848) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_9606ae71-be7a-4996-9110-afd3d2837642) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_39906cec-121a-4f73-887c-5284ea879161) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_2f03de81-6254-4e2f-8ccc-cc280d12dac6) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_f60f13a7-c656-480f-aede-8d7682b4e865) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_9f548d33-f41a-43a7-91ee-b9a3e5db2ab8) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_60e18e91-9ac6-47e1-b5f9-fac4f139166c) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_9d32927b-e3b0-40f1-900e-95967b77260c) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_efc9b9f1-8f04-43fb-85b9-59e61a811510) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
Update (Site_7C6187B3-6719-45B7-AE14-7ED00AF93C57/SUM_ce139a08-1181-42c0-b65d-5defd7ef8bf5) added to the targeted list of deployment ({6C2B0444-BEC6-412D-B50F-C3DFC88BC957}) UpdatesDeploymentAgent 9/3/2015 9:34:01 AM 15740 (0x3D7C)
User logon system task UpdatesDeploymentAgent 9/3/2015 9:53:26 AM 12132 (0x2F64)
EnumerateUpdates for action (UpdateActionInstall) - Total actionable updates = 0 UpdatesDeploymentAgent 9/3/2015 9:53:47 AM 15256 (0x3B98)

The Windows update.log looks like this near the bottom.

2015-09-03 09:56:29:172 156 58d4 Agent WARNING: Failed to evaluate Installed rule, updateId = {{22FFD207-0EB5-4FCF-9F6A-67078327D7A3}.200}, hr = 80070057
2015-09-03 09:56:29:172 156 58d4 Agent WARNING: Failed to evaluate Installed rule, updateId = {{A4ECF96E-FE76-4933-B1A9-FAA712DC2A3B}.200}, hr = 80070057
2015-09-03 09:56:29:172 156 58d4 Agent WARNING: Failed to evaluate Installable rule, updateId = {{A4ECF96E-FE76-4933-B1A9-FAA712DC2A3B}.200}, hr = 80070057
2015-09-03 09:56:29:172 156 58d4 Agent WARNING: Failed to evaluate Installed rule, updateId = {{9941EB5F-4953-446D-99A2-C5989C596283}.200}, hr = 80070057
2015-09-03 09:56:29:172 156 58d4 Agent WARNING: Failed to evaluate Installable rule, updateId = {{9941EB5F-4953-446D-99A2-C5989C596283}.200}, hr = 80070057
2015-09-03 09:56:32:078 156 58d4 PT +++++++++++  PT: Synchronizing extended update info  +++++++++++
2015-09-03 09:56:32:078 156 58d4 PT  + ServiceId = {3DA21691-E39D-4DA6-8A4B-B43877BCB1B7}, Server URL = http://server.company.ORG:8530/ClientWebService/client.asmx
2015-09-03 09:56:32:093 156 58d4 IdleTmr WU operation (CAgentProtocolTalker::GetExtendedUpdateInfo_WithRecovery) started; operation # 53; does use network; is at background priority
2015-09-03 09:56:32:093 156 58d4 IdleTmr WU operation (CAgentProtocolTalker::GetExtendedUpdateInfo_WithRecovery, operation # 53) stopped; does use network; is at background priority
2015-09-03 09:56:32:172 156 58d4 Agent  * Found 0 updates and 78 categories in search; evaluated appl. rules of 1081 out of 1665 deployed entities
2015-09-03 09:56:32:172 156 58d4 Agent Reporting status event with 268 installable, 52 installed,  0 installed pending, 0 failed and 0 downloaded updates
2015-09-03 09:56:32:172 156 58d4 Agent *********
2015-09-03 09:56:32:172 156 58d4 Agent **  END  **  Agent: Finding updates [CallerId = AutomaticUpdatesWuApp  Id = 4]
2015-09-03 09:56:32:172 156 58d4 Agent *************
2015-09-03 09:56:32:172 156 58d4 IdleTmr WU operation (CSearchCall::Init ID 4, operation # 50) stopped; does use network; is not at background priority
2015-09-03 09:56:32:172 156 58d4 IdleTmr Decremented idle timer priority operation counter to 1
2015-09-03 09:56:32:172 156 83d0 AU >>##  RESUMED  ## AU: Search for updates [CallId = {1412030B-55F5-4EC2-BDEB-26162E5D4B80} ServiceId = {3DA21691-E39D-4DA6-8A4B-B43877BCB1B7}]
2015-09-03 09:56:32:172 156 83d0 AU  # 0 updates detected
2015-09-03 09:56:32:172 156 83d0 AU #########
2015-09-03 09:56:32:172 156 83d0 AU ##  END  ##  AU: Search for updates  [CallId = {1412030B-55F5-4EC2-BDEB-26162E5D4B80} ServiceId = {3DA21691-E39D-4DA6-8A4B-B43877BCB1B7}]
2015-09-03 09:56:32:172 156 83d0 AU #############
2015-09-03 09:56:32:172 156 83d0 AU All AU searches complete.
2015-09-03 09:56:32:172 156 83d0 AU AU setting next detection timeout to 2015-09-04 14:05:37
2015-09-03 09:56:32:172 156 83d0 AU Adding timer: 
2015-09-03 09:56:32:172 156 83d0 AU    Timer: 31DA7559-FE27-4810-8FF6-987195B1FD98, Expires 2015-09-04 14:05:37, not idle-only, not network-only
2015-09-03 09:56:32:172 156 83d0 AU  # Publishing WNF Per user update count event Count: 0 SID {S-1-5-21-3477532476-396596822-3023499157-21642} Service {117CAB2D-82B1-4B5A-A08C-4D62DBEE7782}
2015-09-03 09:56:32:172 156 83d0 AU WARNING: Failed to get Network Cost info from NLM, assuming network is NOT metered, error = 0x80240037
2015-09-03 09:56:32:172 156 83d0 AU WARNING: Failed to get Network Cost info from NLM, assuming network is NOT metered, error = 0x80240037

According to the log, there are no required updates on the client.  Because of this, they would not download into the clients cache and would instead reply back to SCCM that they are compliant.

EnumerateUpdates for action (UpdateActionInstall) - Total actionable updates = 0
UpdatesDeploymentAgent 9/3/2015 9:53:47 AM
15256 (0x3B98)

Did they ever show up in the software center on the client computer?  Were all of the updates in your deployment already installed or not required?  This kind of sounds like the case.

That can't be.  I've deployed to 26 Windows 2012 Servers and none of them are running the patches.   And I know that some of these servers have not been patches in over 1 year.  I've logged onto many of them and the last know patches were from 2014.   

in CM2012 I have downloaded all the latest patches.  MS15-90 is the bulletin ID on the most resent.   

On one of the servers in question I viewed the windowsupdate.log and it seems to think updates were there yet nothing gets installed or downloaded.  

2015-09-03 11:10:31:280 876 2450 Agent  * Added update {014486BE-6564-42D1-911C-F961C23A7667}.201 to search result
2015-09-03 11:10:31:280 876 2450 Agent  * Added update {8452BAC0-BF53-4FBD-915D-499DE08C338B}.208 to search result
2015-09-03 11:10:31:280 876 2450 Agent  * Added update {DBE883C8-4D15-4B1D-B8C7-E05D6B557AD3}.202 to search result
2015-09-03 11:10:31:280 876 2450 Agent  * Added update {759396CD-6805-4B93-BB95-20E48BDCAC26}.203 to search result
2015-09-03 11:10:31:280 876 2450 Agent  * Added update {83F6EDCE-C5AA-4A74-935C-5CB24EDE4700}.200 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {D6C864D6-B283-4404-BD46-9FE434FB8356}.202 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {7CE151DE-1480-4B57-AF7C-FAF96BDD2FAC}.201 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {498444E5-F906-41E0-BCC8-FCAA18D384A0}.200 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {0D154DE8-4D10-494D-B9F7-C758A49ECED4}.201 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {04D04AED-7603-420A-A946-96A56D297995}.205 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {5B1464ED-F96E-4845-A714-2E764C18F1D6}.202 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {5F5B21EF-1268-41A1-B043-FDCCD10CD7C9}.203 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {68568DFA-C35C-4BC3-8996-74A818D0E5D7}.200 to search result
2015-09-03 11:10:31:281 876 2450 Agent  * Added update {0CA335FC-58EC-46DE-83D8-44E04052A098}.200 to search result
2015-09-03 11:10:31:327 876 2450 Agent  * Found 69 updates and 73 categories in search; evaluated appl. rules of 1131 out of 1702 deployed entities
2015-09-03 11:10:31:333 876 2450 Agent Reporting status event with 108 installable, 33 installed,  0 installed pending, 0 failed and 0 downloaded updates
2015-09-03 11:10:31:334 876 2450 Agent *********
2015-09-03 11:10:31:335 876 2450 Agent **  END  **  Agent: Finding updates [CallerId = CcmExec  Id = 2]
2015-09-03 11:10:31:335 876 2450 Agent *************
2015-09-03 11:10:31:335 876 2450 IdleTmr WU operation (CSearchCall::Init ID 2, operation # 19) stopped; does use network; is not at background priority
2015-09-03 11:10:31:336 876 2450 IdleTmr Decremented PDC RefCount for Network to 0
2015-09-03 11:10:31:336 876 2450 IdleTmr Decremented idle timer priority operation counter to 0
2015-09-03 11:10:31:405 2976 5180 COMAPI >>--  RESUMED  -- COMAPI: Search [ClientId = CcmExec]
2015-09-03 11:10:32:010 2976 5180 COMAPI  - Updates found = 69
2015-09-03 11:10:32:010 2976 5180 COMAPI ---------
2015-09-03 11:10:32:010 2976 5180 COMAPI --  END  --  COMAPI: Search [ClientId = CcmExec]
2015-09-03 11:10:32:010 2976 5180 COMAPI -------------
2015-09-03 11:10:31:447 876 51ac Report REPORT EVENT: {CB0A914B-1163-415B-BAFF-C604C009C8E3} 2015-09-03 11:10:31:333-0700 1 147 [AGENT_DETECTION_FINISHED] 101 {00000000-0000-0000-0000-000000000000} 0 0 CcmExec Success Software Synchronization Windows Update Client successfully detected 69 updates.
2015-09-03 11:10:32:258 876 51ac Report REPORT EVENT: {8A0CC4F6-FA3D-4AA7-AC99-2C56A18608B8} 2015-09-03 11:10:31:333-0700 1 156 [AGENT_STATUS_30] 101 {00000000-0000-0000-0000-000000000000} 0 0 CcmExec Success Pre-Deployment Check Reporting client status.
2015-09-03 11:10:32:747 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:32:748 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:32:748 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:32:748 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:32:748 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:32:748 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:32:748 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:10:36:333 876 51ac Report CWERReporter finishing event handling. (00000000)
2015-09-03 11:20:33:913 876 4620 AU ###########  AU: Uninitializing Automatic Updates  ###########
2015-09-03 11:20:33:933 876 4620 WuTask Uninit WU Task Manager
2015-09-03 11:20:33:996 876 4620 Service *********
2015-09-03 11:20:33:996 876 4620 Service **  END  **  Service: Service exit [Exit code = 0x240001]
2015-09-03 11:20:33:996 876 4620 Service *************

You need to check all the update logs

WUAHANDLER, UpdateHandling, updateStore

look in the updateStore and see if you have data like this:

Queried Update (21612c2e-1a55-49a6-8e86-c362af00e830): Status=Installed, Title=Definition Update for Microsoft Endpoint Protection - KB2461484 (Definition 1.205.1374.0), BulletinID=, QNumbers=2461484, LocaleID=, ProductID=e0789628-ce08-4437-be74-2495b842f43b, UpdateClassification = e0789628-ce08-4437-be74-2495b842f43b, ExcludeForStateReporting=TRUE.

That way you know if it seeing the updates on the machine. It is possible to patch the machine with Windows update and SCCM will scan it correctly.  First check the logs to see if it has other issues.

I thought I replied to this.  I was able to fix the issue.  I removed the SUP and WSUS roles.  Rebooted the primary site server.  Then I added the SUP and WSUS roles back.   This fixed the issue and we now have all updates through Aug of 2015.

thank you.  

Remove/Install not the recommended way to do it,instead you could have drilled down through the logs on the client and on the server to find the root cause before taking/doing such huge changes.