Hmmm... Something sounds a bit strange. Try manually fsck-ing the drives. Also, try going into your config.ini and verify your settings. See what kind of memory reserve you have, any applications that are loaded that may be logging or keeping the drives spinning. I would almost recommend backing up your existing config.ini and putting a clean one in its place (not loading any additional software or memory tweaks) just to see if it makes a difference. Also try inserting a forced spindown time to see if it changes things.