This will tell you more click here
You can check to see if your drive is definitely flagged by opening up a CLI Window (Start menu -> Select Run -> type in CMD)
Now type in the following:
FSUTIL DIRTY QUERY C: (followed by the enter key)
(assuming that C: is your boot drive)
If it tells you that your drive is dirty then...
Go back to the CLI window and type in the following
CHKNTFS /X C: (followed by the enter key) - This will stop the disk check on the next reboot
Now reboot your computer: let it reboot and open up another CLI - type in the following:
CHKDSK /F /R C: (followed by the enter key) - Let is scan and check your computer fully
Once it has done so type in the following again as in the first step
FSUTIL DIRTY QUERY C:
The drive bit will be set to clean again
Be aware the checking can take some time so ensure you are on mains with no shut down set for period of non-use. DO NOT interrupt the process as you could easily make things worse.