I had Vista bite me in the ass once or twice because of an automatic check disk. In my case, I had XP on a separate drive so Vista decided it would be a good idea to take ownership of every file on the XP disk and completely borked XP so I couldn't boot up any more. Trying to recover XP after this nightmare was worse than any virus you can imagine.
Here's a good solution:
http://www.windowsreference.com/wind...rtup-in-vista/
It's easy to disable chkdsk so you don't have to worry about it fixing things for you.



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