Are all noise filters created equal?

Are you using high quality RCA's?

One thing that I know about Pioneer units is that they internaly ground their preamp outputs and that has been an issue with their units for many years. The last 2 Pioneer decks that I had both had noise issues. One way that I got rid of the noise was to reground the RCA's near the amps. That worked for the 7600 unit that I had. The 8600 that I had also had noise issues and I never delt with it, I just returned it and went with Alpine and never had an issue after.

Chris

Sounds like you definately have a HU issue.  Pioneers are notorious for poor internal ground plane quality and often the only way to fix this is by swapping head units.  I assume yours is under warranty?

Since you've already tried about everything you can with your amps, try a dedicated ground for the HU that is not part of the car's wiring system.  Try grounding the outer ring of the RCA cables.  Like haemphyst said, don't waste your time with noise filters, they do nothing but mask part of a problem and degrade your sound quality.

If the above does nothing to help with your problem, take the head unit back and swap it for another one.