Yeah. Must be Microsoft's fault. Format and install linux.
I hate Microsoft as much as anyone, but chances are the problem was caused by a broken worm spread using one of the vulnerabilities Microsoft patched
I really, really doubt MS would release a patch that would cause filesystem damage. A worm, on the other hand, could be trying to hide itself and screwing up the filesystem in the process.
Imagine a pathologically idealistic, anti-religious, culturally-relativistic, iconoclastic, socially-irreverent, sociologically-progressive signature line here. Or don't.