Does CHKDSK ever detect any problems on boot?
When you are in Windows 7, open up the command prompt in admin mode (find it on the start menu then right click > run as administrator). Then run the following command on all your drives (replace x: with each letter):
That should list any "dirty" drives.
Now, type chkntfs /x x:. The /X tells Windows to NOT check that particular drive on the next reboot. Now manually reboot your computer, it should not do a chkdsk and should take you directly to normal Windows login.
Once Windows has fully loaded, bring up another admin command prompt and enter chkdsk x: /f /r. Reply Y if asked if you want this to happen on the next boot. This should take you through 5 stages of the chkdsk scan on the next boot and will unset that dirty bit.