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I don't know a whole lot about Windows anymore but I wonder if it would help if you ran chkdisk from the restore dvd? That is if the DVD even allows you to run chkdisk without reimaging.
Your disk is most likely contains corrupt data. I hope it is not getting ready to kick the bucket on you. But if you can repair the errors by booting from any media other than the hard drive, you might be ok.
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-Marcus
1997 4Runner Limited 4x4, E-Locker, Bilstein HDs, Air Springs, Deckplate Mod, 265/75/16R Bridgestone Deuler A/T Revo
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