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Using Windows 7, when I go to Start -> All Programs I can see the full structure and all of the shortcuts, but when I click on one, nothing happens. I navigated to:

C:\Users\myusername\AppData\Roaming\Microsoft\Windows\Start Menu\Programs

and the majority of the "All Programs" structure is missing.

I found if I clicked a shortcut under the "All Programs" menu that also existed in the backend "AppData" tree, everything works as expected.

What would cause Windows to place the program shortcut under Start -> All Programs, but not create an actual shortcut behind the scenes? Is there a registry entry that determines where these shortcuts are created?

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Did these shortcuts exist at some point and are now missing? –  Dave M Jan 18 '13 at 15:17
    
I'm inclined to say they didn't previously exist. Looking a bit deeper I found the other shortcuts reside under C:\ProgramData\Microsoft\Windows\Start Menu Programs. These shortcuts work if I use them directly, but not from the "All Programs" menu. –  Josh Johnson Jan 18 '13 at 15:24
    
I have the same issue, try this superuser.com/questions/651262/… –  malakrsnaslava Sep 27 '13 at 18:58

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