Things to check (Kelly Theriot):
Go to Start/Run/CMD and type in: fsutil dirty query c:
(Modify the drive letter accordingly)
If it comes back as dirty, the dirtybit hasn't cleared. For more information go to Start/Run/CMD and type in: CHKNTFS /?
Optional: From a command prompt type chkntfs /D and then reboot, a chkdsk should then run if shceduled, but not on the next boot.
Go to Start/Run/Regedit and navigate to this key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon
Highlight the Winlogon file.
In the list look for "SFCScan", this should be set to (0) if it is set to (1) the scan will happen at every boot.
Go to Start/Run/Regedit and navigate to this key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager
Look for the REG_MULTI_SZ value with the following name: BootExecute. This value contains commands that will be executed at startup. The default value is: autocheck autochk *
After scheduling one or more chkdsks, the entry will contain one or more autochk lines. Delete each of these lines and put the default one in place.
If you always want a check to be performed at startup, change the value to: autocheck autochk /f *
If you don't want any checks to be performed, delete all autocheck entries.
Modify as needed. The path to the chkdsk utility may be wrong:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\cleanuppath
Registry entry should read: %SystemRoot%\system32\cleanmgr.exe /D %c