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contents of start menu programs missing

After malware removal, the contents of the start menu programs are missing.  All of the programs are listed but the contents are empty.  I ran unhide.exe, I also set the properties of Program Files folder in C: to unhidden.  
The programs are still there and accessible but not visible in start menu from all accounts, adding new accounts also have no files visible within program folders in the start menu.  How to fix this?
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younghv
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It appears that if i start in safe mode, the contents of the programs folders in the start menu are available.  Is there a way to copy these contents into the folders the user uses when they log on to their domain account?
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The system did require additional virus scans.  It appears that the shortcuts were deleted as stated.