I'm a dual booter, Ubuntu 10.04 and Windows 7 (64 bit), and yesterday I was greeted with an irritating problem that was making me pull my hair out (I know, with Windows, huge shock right? :p )When the computer was booting up Windows, I kept getting a message that my C drive needed to be checked for consistency, for no apparent reason. So the message states to press any key to skip the check or let it finish the countdown and the check will begin, well, after multiple attempts either way I can assure you neither happened, all I got was a countdown timer frozen at 1 second remaining.
I will not bore you with all the crap I tried to remedy the situation.
What did finally work for me was this hotfix from Microsoft.
Once that was applied, I still got the Chkdsk message one more time after I rebooted, but this time it didn't freeze, it completed the check, and booted up Windows as it should. All reboots after went without a hitch and the message was gone, all is well. (this lasted a week)
UPDATE:
Ok, the problem eventually came back, why I don't know, but this is how I ended up resolving it as the flag had not been cleared before it seems. To get rid of this issue, just do this:
Click on Start
Then in the Search programs and files box type cmd (do not press Enter)
When cmd appears in a list of results under Programs, right click it and select Run as Administrator. (unless you're already running as Administrator)
Now type fsutil dirty query c: (this tells you if the drive is flagged as dirty)
Then type chkntfs /x c: .
The X in that command will tell Windows not to check the C: drive when it next reboots. Once you reboot the computer manually, it shouldn't do a chkdsk scan, it should just go to the normal Windows login screen.
When Windows has completely finished loading, open another Command Prompt as Adminsitrator (like you did before) and you'll want to enter chkdsk c: /r
When asked if you want this to happen on the next boot of the system reply with Y. Now reboot again and what should happen is you'll be taken through all 5 stages of the chkdsk scan and if all goes well it will reset the flag from dirty to clean. I have a 750GB drive on my computer and it took a few hours to complete, so be patient, it will all depend on many variables, but it could take a very long time. At first it didn't seem like it was doing anything, I thought it had locked up but decided to give it time and sure enough it was fine and completed all 5 stages of the chkdsk scan.
Once the scan has completed and you're back and logged in to Windows again, open another Command Prompt and enter fsutil dirty query c: to make sure the drive now reads as clean when you query it.
Hopefully this can save someone some hair loss

