Read the explanation from the following MSKB article:
Q160963 -"CHKNTFS.EXE: What You Can Use It For", including the cases when chkdsk is disabled for some drives.
So, in essence, you should open regedit and expand the following path:
HKLM is HKEY_LOCAL_MACHINE
In the right pane, look for BootExecute. It's value should be :
autocheck autochk *
If it's not, change it as the above bolded value.
Backup your registry or create a Restore Point before.
Trying to unweave, unwind, unravel
And piece together the past and the future,
T. S. Eliot