This condition is what Windows refers to as "setting the dirty bit" and you have to unset that bit. If the dirty bit is set,then autochk performs an immediate chkdsk /f on that volume. This is usually caused by an unusual shutdown or a power loss during a read/write operation.
This could possibly fix it:
Click Start and type cmd in the search programs and files dialog box. Then type fsutil dirty query c:.
This query will return an answer if your drive is dirty or not. Most likely its dirty
Next, type chkntfs /x c:.
The x tells Windows to not check that particular drive on the next reboot. At this point reboot your computer, it should not perform a chkdsk on startup and take you directly to Windows.
When you are back in Windows you want to do a manual check disk on the c drive, to do this:
Click Start and type cmd
in the search programs and files
dialog box. Now type chkdsk /f /r
This should take you through 5 stages of the scan and will unset that dirty bit.Since this will have to run a checkdisk on your C drive it will ask you to run it on your next restart.
Finally, type fsutil dirty query c:
This will confirm that the dirty bit is not set on that drive. Hopefully this resolves your problem.