I have W7 in two computers. One desktop Fujitsu-Siemens Quad-core in dual system startup mode and LG laptop Core 2 Duo, with W7 like only OS. Frecuently begin with execution of chkdsk without problems.
What you're experiencing is what Windows 7 refers to as "setting the dirty bit" and what you have to do is unset that bit. Every time Windows 7starts, autochk.exe is called by the kernel to scan all volumes to check if the volume dirty bit is set. If the dirty bit is set, autochk performs an immediate chkdsk /f on that volume. Chkdsk /f verifies file system integrity and attempts to fix any problems with the volume. It is usually caused by a hard shut down or a power loss during a read-right operation on that particular drive.
That's easy to fix. First click <Start> <Run> bring up a command prompt by typing in "CMD" and type " fsutil dirty query d: ". This queries the drive, and more than likely it will tell you that it is dirty. Next, type "CHKNTFS /X D:". The X tells Windows to NOT check that particular drive on the next reboot. At this time, manually reboot your computer, it should not do a Chkdsk and take you directly to Windows.
Once Windows has fully loaded, bring up another CMD prompt and type and now you want to do a Chkdsk manually by typing "Chkdsk /f /r d:". This should take you through 5 stages of the scan and will unset that dirty bit. Finally, type "fsutil dirty query d:" and Windows will confirm that the dirty bit is not set on that drive.