I started noticing the same problem about a week after I got my empeg installed. My unit doesn't seem to ground properly sometimes... All I needed to do was wiggle the unit until it was grounded properly.
The car-toys installation guy said that if the empeg is not seated properly then the ground that it uses is probably the RCA shielding > amplifier > amp ground cable. It will pick up noise in the long RCA cables, which lead back to my trunk.

Mk2/40GB/Blue