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in the beggining I would like to mention that I'm REALLY pissed off. I've spent whole night to fix this and today I must go to work.

So I'm unhappy user of Windows 8 I wanted to check my hard drive by using the chkdsk on D and C drives. After next reboot it started and there my nightmare begins. There is NO way to skip that! When C drive checking was complete then my PC restarted and began to scan D. I was waiting for over 4 hours and it just stuck on 27%. I restarted the PC. After this Windows did this damn, annoying automatic repair thing. Ofcourse it didn't help so I have chosen command prompt from troubleshooting section. I typed chkntfs /X C: D: It did not help ... After rebooting chkdsk is checking C: drive agin and I'm afraid that after this it will also try to fix D: drive which is not damaged! How to skip this process?

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You allow it to run. In the future don't run chkdsk unless Windows reports a problem. –  Ramhound Apr 15 '13 at 10:50
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up vote 1 down vote accepted

You can "fix" this problem by not using chkdsk on active partitions. if you try an chkdsk on an active partition, windows will delay this operation until boot time, when it is unmounted and available to be checked AND any possible filesystem damage/corruption is fixed.

It is best to let chkdsk complete its job.

If you are seeing this stuff w/o running a chkdsk directly on an active partition, then I'd say your shutdown is failing properly leaving the disk in an unstable condition which can only be corrected by a chkdsk at startup time. Windows checks for this upon boot to you from mounting a damaged disk causing even more damage.

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