I had some similar noises after my initial install. They're likely to happen anywhere the signal (RCA) lines between the empeg and amp get near to the vehicle's wiring. I cleared mine up simply by rearranging the rat's nest of wires behind the empeg keeping the power wires on one side and the signal wires on the other. There are also RCA cables built specifically for in-car use that have better shielding, you may want to try these.
Also, as a rule of thumb, don't run power and signal wires to your amp via the same route. You're almost certain to get noise that way.

-Zeke

just say you weren't paying much attention...