This T61 is having similar issues under Winders - random freezes for many seconds at a time, with the HD light full on (but no changes in the Google Desktop HD access widget). I'm assuming it's the drive, too, though nothing systematic has shown up in chkdsk, Windows logs, etc. No viruses, no help in turning services off, etc. It's annoying.
It doesn't seem to have any problems with Ubuntu 10.04, so I think it's a problem with the Winders partition..
I got a 640GB Samsung to swap in, but haven't done the backup and cloning yet.
I'm glad yours turned out well - thanks for the linky. Fingers crossed here...
Cheers,
Scott.