Thats not good. You comp is running chkdsk because it thinks there is a problem with your HD (Usually your computer is right about that). Try to boot into safe mode (F* on startup) click start - run "cmd" type "chkdsk /r" "Y" to confirm. Shutdown your computer (Dont restart) Turn back on let chkdsk run. If you are still having issues download Hitachi Drive Fitness Tester burn to CD and test you HD. Good Luck.
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