Have the "Power down disks" option set to 5 minutes. Disks never power down. Have four 1.5tb Samsung drives in RAID5 config. Just updated to 220.127.116.11736 firmware. Was not working with factory installed firmware either. Any idea why the power down option is not working?
I'd check to make sure they were on the tested list at http://www.intel.com/support/motherboards/server/ss4200-e/sb/CS-028561.htm. If the disks aren't powering down, and they're on the list, there's something that's writing to them at intervals shorter than 5 minutes.