It may be that your ground is not grounded properly...
I had thought of that... and I will try it again if I can find another possible grounding point, but...
The empeg used to get its connections via a T-Harness made especially for Hondas (in order to keep the keyless entry which is housed inside the factory radio). I have sacrificed keyless entry (never used it anyway) in order to have my empeg. When using the T-Harness, the empeg and the CD receiver were grounded on the same ground line (going through the standard Honda wiring harness), but at different points on the line. This minimized noise greatly. However, when they were grounded to the same point on the line, I experienced noise similar to what I have now.
I am quite sure that I have to find a better ground for the empeg, and possibly its docking sled. But with its recent behavior after giving it a direct line to the battery, I also feel the noise may have something to do with that new connection. Is there some way to minimize or kill noise that might be coming down the power line?