Do you mean its running Scandisk/chkdsk or do you mean the Windows System File Checker is running? What's on your screen?
If SFC is running have a look at -
http://support.microsoft.com/default...b;EN-US;310747 - the registry key may be bollixed.
Take a look at Settings/Control Panel/Administrative Tools/Event Viewer/System and look through the Errors and Warnings (some of these are not significant, but you may be able to pin it down by time).
Your HDD is a bit small and elderly - having just had a heavily used WDD drive fail on me (only second HDD failure ever), I wonder a bit about the drive's health. If you have SMART tunrned on in the BIOS it will warn you of impending drive failure on botup (the WD200BB is SMART enabled).
Good luck
