Usually engine noise is due to a loose connection somewhere, typically a ground wire. Every once in a blue moon it's a bad alternator or voltage regulater, or some other random crap, but from what I've seen that's not the norm.

I would try pulling the sled out far enough so that you can get to the cables, and then fiddle with all the connections while it's playing. Just be careful not to ground out a 12v lead or anything. (No power wires should be exposed, but it never hurts to be careful.)

More than likely, you'll find there's one connection back there somewhere that's just a little sketchy.

I had the exact same problem with my empeg. On my unit, it was where the cables connect to the molex on the back of the sled.