Before you shutdown, use Regedt32 to navigate to:

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager

Double-click the BootExecute value name in the right hand pane and change the string from:

autoconv \DosDevices\<Drive:> /FS:NTFS

            TO

autocheck autochk *

NOTE: This tip works for Windows NT and Windows 2000