Have you ruled out some sort of software issue? Random programs will cause stuff to shut to and act weird. Try installing SpeedFan and using the diagnostic tool it has for your HDD.
http://www.almico.com/speedfan.php
Under the S.M.A.R.T. tab, select your Drive, and do the in-depth online analysis. Any issues will be listed - specifically a bad sector count. Do it for both HDDs and post up the results if you want. After reading what you are describing and listening to the video you posted, I still don't think it's a HDD problem (and apparently others don't either).
http://www.almico.com/speedfan.php
Under the S.M.A.R.T. tab, select your Drive, and do the in-depth online analysis. Any issues will be listed - specifically a bad sector count. Do it for both HDDs and post up the results if you want. After reading what you are describing and listening to the video you posted, I still don't think it's a HDD problem (and apparently others don't either).