I was helping another empeg owner (Russmeister) this weekend with trying to get rid of the alternator whine in his system. We double and triple checked all wiring, regrounded all the amps, the sled, the player, etc...with no dice. Also tried adding a ground loop isolator...still no dice.

Finally we fixed the problem. We ended up taking the amp apart and soldering a ground wire from the ground on the circuit board to the ground on the RCA inputs in the amp. After doing that, it worked like a charm!

Don't know if that'll help in your situation, but it's something else to try.