I have created 2 USMT task sequences.   TS Num1:   Has 3 steps, request state store, capture user state, release state store.    

task sequence Num 2:  Has 3 steps, request state store, restore user state, release state store.  The first step, request state store has the following setting.    "Restore State From Another Computer"

I run TS Num1 on my SOURCE.  I run TS Num2 on my TARGET.     now, here is the strange part.    Before I reboot my Target machine I check to see if my profile was created.  It was.  I then check the c:\users\NewProfile\Desktop folder and I see all of my Shortcuts.  I also see a Folder I created and inside of this folder I see more shortcuts.

I then reboot.  I log in as NewProfile and my desktop only has the folder with shortcuts.  All of the other shortcuts have been deleted.  Why?  They were there.  There is nothing in the log files since the TS ended.   Why would only the desktop shortcuts get deleted?  The desktop folder remained and it has many shortcuts inside of it.  All of my .DOC files in "My Documents" are there as well.   Only the desktop shortcuts are gone.

I read this about USMT and shortcuts.    By default USMT always tries to copy shortcuts for files that exist on the destination computer during loadstate, 

All of the shortcuts on my desktop that get deleted do have working paths on the Target machine.   The shortcuts are for Word, Excel, PowerPoint and a few other apps that are on All Builds.  So they should be getting copied yet they get deleted.