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I'm not sure if this will work with a raid setup, but it should disable chkdsk at startup.
Boot with a boot disk and at the command prompt type
fsutil dirty query c: [enter]
chkntfs /x c: [enter] (/x prevents chkdsk from running on c:)
Remove the bootdisk and reboot.
chkdsk /f/r c: [enter] (/f to fix errors, /r to find bad sectors and recover data)
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TSF Folding@Home Team 85015 - details here
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