The best way (and IMO only real way) to run a checkdisk is offline through an install disc. Vista and XP both have the option to run chkdsk from their install discs.
XP:
Boot to any XP install disc
At the first screen hit “r” to enter Repair Mode
Type number associated with Windows install
Type password for admin account (default is none)
type “chkdsk c: /r /f”
When it’s done, reboot.
Vista:
Boot to any Vista install disc
At the first screen click Next
Click Repair your computer
Select the OS and click Next
Cancel any automatic repairs
At the recovery menu, click Command Prompt
Type “chkdsk c: /r /f /x” (note that the /x allows you to force the volume to dismount when it’s not running an OS)
When it’s done, reboot.
Even if you have XP installed, if you can get your hands on a Vista install disc use it for ANY repairs or offline changes you need to make. Vista may suck at repairing itself but it’s command prompt is almost magical.