Noise is being picked up by one or both your receiver's power leads. Install a noise filter on one or both of the leads.

I used a 20-amp noise filter from Radio Shack, and it's installed on the main power lead that comes straight from the battery. My Empeg and amps are both powered from this lead. This did significantly reduce the noise in my system immediately after I installed it.

Also, check to make sure there aren't any loose wires on the docking connector, or elsewhere in the system.
You mean the AUX and serial connectors? Yes, they are loose. Should I seal them or cut them off?

No, I meant are there any bad/frayed/intermittent connections at any point in the system. Including the wire ends that were crimped into the docking connector at the factory.

My installer did confirm to me that he routed the power cables and audio cables on separate sides of the car, though.

Confirm this yourself, don't take their word for it. And remember- it's just as important for the audio cables to be routed away from all other car wiring, not just your amplifier's power wires.

Maybe I'm just being too fussy, maybe there is some amount of noise which just needs to be accepted. The noise I am hearing can only be heard at low volume, or when the player is paused. If the volume is cranked up, the noise cannot be heard.

If your amps have their gains properly adjusted, you should not hear any noise when the player is playing with the volume turned all the way down. Remember that you should be able to play your empeg at 0db (maximum non-overdrive volume) without damaging your ears or your speakers. If you can't turn up the Empeg that loud, then you've just got your amps set too high.

Other things to try: Methodically eliminate all components that might be causing the problem. For example, disconnecting the car phone stuff temporarily. If there's an EQ or crossover in the system, try removing that, etc. Try lifting grounds. Try adding grounds...

It might take some work to elimintate the noise, but eventually you'll be able to get there.

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Tony Fabris