Since updating to Mountain Lion, including 10.8.1, my two Elements desktop drives, each 2 TB, go idle very soon after disk activity, and take several seconds to revive once another disk transaction is attempted. There does not appear to be a firmware update for these drives. It would be great to know that a solution is forthcoming, even if it involves waiting patiently for 10.8.2. Thanks.
Don’t know a lot about Macs, but check if you have the option to disable sleep mode for the hard drives.