First you can try to boot to a Safe Mode Command Prompt only and run a chkdsk /r C: to try and clear the "dirty bit".
You can also try a registry edit. Open regedit from Start and Run then regedit and click Ok. Navigate to the HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager key. Find the BootExecute value and double click it. Remove all lines of text from the box.
**Do so at your own risk and backup the registry first because editing the registry can cause you computer to become inoperable.**
You can also try a System Restore and go back to a point before the problem started.