Disabling Chkdsk - Windows 2000 and XP
1. Run the Registry Editor (regedt32.exe)
2. Under the HKEY_LOCAL_MACHINE subtree, go to the following subkey:
\SYSTEM\CurrentControlSet\Control\Session Manager
3. Change the BootExecute entry to:
autocheck autochk *
Exit your registry, you may need to restart or log out of Windows for the change to take effect.
(Link)
http://www.dataclinic.co.uk/disable-scandisk-chkdsk.htm
Also yes it very well could be your harddrive. Sounds to me a very much like a bad hdd is signaling Windows to start up chkdsk, which in turns finds bad sectors and marks them as bad or as your concerned deletes them. Anyway this is all on the assumption this is chkdsk running. Honestly I have not run the program myself in a very long time so I don't really remember the message it gives. I would give this app a try;
http://support.wdc.com/download/?cxml=n&pid=999&swid=3 (datalife gaurd)