At the command prompt type fsutil dirty query c: (or the relevant drive letter). 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.
Reboot, it should load to the desktop
Once Windows has loaded bring up another CMD prompt and type Chkdsk /f /r c:
This should take you through the 5 stages of the scan and will unset the dirty bit.
At a command prompt, type fsutil dirty query c and Windows will confirm that the dirty bit is not set on that drive.