Windows 7 - Programs Missing

My user contacted me regarding the issue that all of his Program shortcuts that were in the start menu are now missing. Please see attached file.

I'm not sure what caused this or if he did something to cause it but any quick advice on how to fix this would be greatly appreciated.

I already tried the Default Settings on the Customize Start Menu option.

Windows 7 x64 Professional
Helping_AlmacAsked:
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Helping_AlmacConnect With a Mentor Author Commented:
I was able to see that somehow the folder at this path

C:\ProgramData\Microsoft\Windows\Start Menu had it's rights changed. So I had to uncheck the read-only box and apply the settings to the folders under it. I'm not sure how the user changed that setting but all is fixed now.

Thanks everyone for your input.
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aadihCommented:
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Helping_AlmacAuthor Commented:
There's a lot of home grown folders that are missing also. Will this help address that issue as well?
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aadihCommented:
Well, try a system restore to an earlier point; and then run Malwarebytes Antimalware; and use a good security program as a real time protection (what is the current program?).
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Helping_AlmacAuthor Commented:
We disable system restore during our setup. This is a laptop that's protected under Sophos Endpoint.
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Darr247Commented:
Sounds like malware. Probably disabled windows firewall and removed the Base Filtering Engine service, too. (click 'start', type in services.msc and hit Enter to check).
 
If that's the case, you can try to clean this, but you'll never be sure you fixed everything that malware damaged. Probably faster and safer to backup the user's data, wipe the machine and reinstall windows (or restore your image), and programs, then restore the user's data.

I use MalwareBytes Anti-Malware Pro in protection mode to stop malware like that in its tracks (you can enable that for a couple weeks in the free version to try it)... your mileage may vary.

There was no attachment on your message, by the way... after browsing to and selecting the file, you still have to click the Upload File button when you're back at the Comment box here in order to finish the attachment process.
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aadihCommented:
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Helping_AlmacAuthor Commented:
Sorry here's what the desktop looks like.
MissingPrograms.JPG
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Helping_AlmacAuthor Commented:
I don't believe this was malware - I was comparing my settings on my folder structure and noticed that the user who was having the issue had the StartMenu with a lock symbol. I was able to uncheck the read-only for that folder and apply it to the subfolders. After doing so the programs populated onto the Start Menu.
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