I recently tried to run CHKDSK /R on a computer, and it would not run. After the computer restarts, the typical 10 second countdown would stop after one second. I saw a message like "Chkdsk - disk checking has been cancelled".

After several Google searches, it seems this happens to others - but there are few solutions. I found the solution on a Microsoft forum:
Can't run chkdsk on windows 7 - chkdsk cancels 1 second into countdown

---------------------------------------------------------------------------------

"First thing to check msconfig.  Go to the boot tab and make sure that "no GUI boot" (or something similar to that) is NOT checked!  Save but do not reboot yet.

Next go to a command prompt.  Do not paste the pound sign or anything after in the line.  Note that there are 3 programs being run

chkntfs /d
#this resets the chkdsk and autochk settings to default

chkntfs /t:0
#this sets the timer to 0 seconds...so things will run before they can be cancelled.  You MIGHT be able to get away with /t:1, which would allow you to manually cancel, but I doubt that would work.

chkntfs /c C:
#tells it what drive to check

chkdsk /r
#implies /f.  basically look for and fix everything

fsutil dirty set c:
#forces a check on the disk at the next boot.  Probably not needed if you are running a scandisk because your computer thinks it might have a problem.

now you're FINALLY ready to reboot."

---------------------------------------------------------------------------------

Here is the text of a BAT file that I created, with the comments embedded, and lots of PAUSE statements

REM this resets the chkdsk and autochk settings to default
chkntfs /d
pause

REM this sets the timer to 0 seconds...so things will run before they can be cancelled. You MIGHT be able to get away with /t:1, which would allow you to manually cancel, but I doubt that would work.
chkntfs /t:0
pause

REM tells it what drive to check
chkntfs /c C:
pause

REM implies /f. basically look for and fix everything
chkdsk C: /r
pause

REM forces a check on the disk at the next boot. Probably not needed if you are running a scandisk because your computer thinks it might have a problem.
fsutil dirty set C:
pause

REM now you're FINALLY ready to reboot."
pause
C:\Windows\System32\shutdown.exe -r -t 04 -c "ReBoot!!"

Last modified: December 23, 2016