Open a command prompt as Administrator (method 1) click here
At the prompt, type FSUTIL DIRTY QUERY C: and press Enter. This queries the drive, and more than likely it will tell you that it is dirty. Next, type CHKNTFS /X C: The X tells Windows NOT to check that particular drive on the next reboot. At this time, manually reboot your computer, it should not do a Chkdsk and take you directly to Windows.
Once Windows has loaded, open a Command Prompt window again and perform a Chkdsk manually by typing CHKDSK /F /R C: This should take you through 5 stages of the scan and will unset that dirty bit. Finally, type FSUTIL DIRTY QUERY D: and Windows should confirm that the dirty bit is not set on that drive.