I've been repairing a Windows 7 64-bit installation. In the process, the Windows partition was subjected to several rounds of automatic repair,
sfc, even a volume shrink. Long story. Anyway, after I'm done, Windows mostly works, but it seems that all NTFS junction points - like
c:\Users\Username\Start menu - are not junctions anymore, they're just empty folders.
I can't really tell on which stage did this happen. Stages were many, and Windows won't boot in the meantime. The filesystem on the partition was NTFS all along though.
Is this a known condition, is there a wholesale solution to this? Barring that, is there a user profile fixing routine which restores the proper folder/junction/permission structure?