Windows XP
Start>Run>chkntfs /x <drive> [drive] [drive]
For example, if you want to disable Chkdsk from running on drive C: chkntfs /x c:
Chkntfs works by modifying the BootExecute value in the Registry.
HKEY_LOCAL_MACHINE\SYSTEM\CURRENTCONTROLSET\CONTROL\Session Manager
The default value is BootExecute:REG_MULTI_SZ:autocheck autochk *
Chkdsk /f /r is unaffected by chkntfs and can be run to check volumes manually on the next system reboot.
This from:
http://www.marvswindowstips.com/on_off.htm
Looks solid to me.