Start Menu items/shotcuts and Start Menu search ability on multiple workstations

2/13/2014 our IT department began to receive complaints of missing programs. After investigation of a few users we were able to determine that the programs existed but all shortcuts and items from the start menu had been completely removed. In addition the
searching feature of the start menu was not functional. This happened to about 90% of our environment and the catalyst seemed to be Windows updates or at least occurred after the auto reboot initiated by Windows Updates.  The only items visible in start
menu were items added after the fact, internet explorer, magnifier, command prompt, and notepad. All other items, folders, and the ability to search installed programs or folders were completely removed. However all programs are present in the program files
folders. THe start menu folder in program data was empty except for the aforementioned items. Additionally properties of start menu had all necessary checks in boxes such as search program files and folders etc. Also show hidden items and folders is enabled
for many users so the items were not hidden but gone. And the biggest kicker of all was after a full domain investigation into the issues we found that the majority of our windows server platforms, primarily 2008, were also affected and system restore is unavailable.
This conflicts with our idea that Windows Updates caused this since our servers get their updates on a manual initiated basis by their admins which we have not performed as of yet for this month. This caused me to begin looking at SCCM SCEP as all systems
have System Center Endpoint Protection and received definition updates. Also accessing different user profiles or even a new profile did not make a difference, issue still present.
Due to the enormous inconvenience we sent out a company wide email asking users to perform system restores to get us in a stable state. A system restore to the day before Windows updates (second Wednesday of every month configured by SCCM SCUP) restored
the start menu items.
On a multitude of machines IT performed troubleshooting and system restores recording the changes removed and added. We then, on a healthy machine, started to apply the windows updates and SCEP (antivirus) definitions 1 by 1 with out success of replicating
the issue. Next we performed a system wide antivirus full scan and did not find any viruses. This is obviously not a system criticle issue bringing us down but is a huge concern for us in IT as it happened company wide and caused a large flux of tickets and
some down time for non-technical users. We most definitely want to know the cause and after several days of investigation and troubleshooting Im turning to the Microsoft community for help.
I know I categorized this as a Windows 7 issue and its affecting windows server 2008, 2003, and 7, but I did not see a forum for all windows platforms. Since the majority of affected users are Windows 7 I opened it here.
So to summarize in a bulleted format:
Issue: Wide spread issue affecting around 60-70 users and servers, all profiles, were all start menu items save one or two system defaults were removed. Additionally the searching feature for the start menu looks to be broken as programs
exist in program files and are unsearchable from start menu. IT was also affected and I remain affected until I find the cause.
Investigation and Troubleshooting:
Start menu properties: nothing has changed and search options are enabled.
Missing items are not hidden, hiding and unhiding does nothing and folder options show hidden files is checked.
Program data start menu location is indeed empty as well as user app data start menu location
No group policy's are in place altering start menu items and no group policy changes were made as of recent
No SCCM packages pushed company wide in last month or pushed individually
Windows Updates occurred on windows 7 machines only before the issue occurred and computers restarted and the issue surfaced
System Center Endpoint Protection Antivirus updates and definitions deployed just before the occurrence with windows updates. SCEP def updates happen on all windows boxes to include servers
Paint.exe was completely missing from system32 folder for some users machines to include my own
System restore to that morning before restarts or previous day fixes the issue for windows 7 users
No windows updates were initiated on any servers
Servers were also affected with windows 7 machines
About half the users affected had corrupt Microsoft Office 2013 Pro Plus Click to Run installations and for some the system restore did not fix this and we had to re-install office for around 10 users
SCEP antivirus did not catch any viruses that could cause this, I performed MBAM scans on a handful of machines and didn't find anything either.
Re-creating start menu shortcuts works
Happened to two of our companies locations NH and MA, all part of the same domain but different LANS of course. Companies are interconnected by MPLS connection.
I combed through SCCM to see if anything deployed and found nothing. Currently I have SCUP updates and SCEP updates disabled. I will post a list of Windows Updates that occurred when the issue occurred as well as the SCEP updates. I have read all the threads
about this types of issues and tried all steps without success. Googling the issue also did not rear results.
MichaelSpaulding

Hi,
I would like to suggest you try these steps to figure out what could be causing this problem.
1. Run Troubleshooter
Open the Search and Indexing troubleshooter
http://windows.microsoft.com/en-US/windows7/Open-the-Search-and-Indexing-troubleshooter
2. Create a new library and include fewer folders for test purpose. Now search for a file from that folder. See if it works.
Create a new library
http://windows.microsoft.com/en-US/windows7/Create-a-new-library
3. Try to rebuild search indexing. Refer the steps from the following article.
http://windows.microsoft.com/en-US/windows7/Change-advanced-indexing-options
Also you may use the System File Checker tool (SFC.exe) to check the issue. The sfc /scannow command scans all protected system files and replaces incorrect versions with correct Microsoft versions.
How to use the System File Checker tool to troubleshoot missing or corrupted system files on Windows Vista or on Windows 7
http://support.microsoft.com/kb/929833
In addition, you may refer to the following Microsoft TechNet article for the Windows Search related Group Policies.
Group Policy for Windows Search
http://technet.microsoft.com/en-us/library/cc732491(WS.10).aspx
Hope it helps.
Regards,
Blair Deng
Blair Deng
TechNet Community Support

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