Maybe you are having this problem where chkdsk "thinks" you pressed a key to cancel it - this will let you test that theory.
I would do all these things from the Command Prompt opened as Administrator:
Click the Start orb/button and in the box enter the following:
cmd.exe
Right click cmd.exe and choose to Run as Administrator:
First reset the Windows autochk settings to their default value to undo any failed efforts, trying things or other adjustments that might have been made by entering this command:
chkntfs /d
Remember that command since it resets any adjustments you might make later and sets things back to "normal".
If you enter this command it will tell you how long Windows is going to give you to press any key to cancel the chkdsk:
chkntfs /t
You can see that the default is 10 seconds:
For some unknown reason your system "thinks" you pressed a key to cancel the chkdsk so you can tell it not to give you any chance to cancel the chkdsk by entering this command (set the time to zero seconds):
chkntfs /t:0 (that's a zero)
Now schedule your chkdsk with error correction to run on the next reboot with this command (which you already know):
chkdsk c: /r
Now restart and see if the chkdsk with error correction will run... and it could take a long time depending on the speed of your system, the size of the HDD, the amount of data on the HDD and what the chkdsk finds to do.
Do not interrupt the chkdsk - it will finish one way or another sooner or later.
If you want to set the countdown timer back to 10 seconds issue the following command:
chkntfs /t:10
That doesn't explain why Windows thinks there has been a key pressed but you might figure that out later.