This is similar to 008 » Stop CHKDSK from running at boot time.

Use Regedt32 to navigate to:

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager

Double-click BootExecute in the right-hand pane. In the Multi-String Editor, change:

autoconv \DosDevices\ /FS:NTFS

         TO

autocheck autochk *

See tip 0320 for the space required to perform a convert.

NOTE: If you have an additional drive or partition, see tip 1377.