Chkntfs is designed to disable the automatic running of chkdsk on specific volumes, when Windows restarts from an improper shutdown. Chkntfs can also be used to unschedule a chkdsk if chkdsk /f was used to schedule a chkdsk on an active volume on the next system restart.

Every time Windows restarts, Autochk.exe is called by the Kernel to scan all volumes to check if the volume dirty bit is set. If the dirty bit is set, autochk performs an immediate chkdsk /f on that volume.

See -> http://support.microsoft.com/kb/160963

chkntfs /c drive: […]

drive: Specifies a drive letter.
/D Restores the machine to the default
behavior; all drives are checked at boot
time and chkdsk is run on those that are
dirty. This undoes the effect of the /X
option.
/X Excludes a drive from the default boot-time
check. Excluded drives are not accumulated
between command invocations.
/C Schedules chkdsk to be run at the next
reboot if the dirty bit has been set.