Reground your headunit. Your problem is that your amp has a better ground than your HU and your signal cables are not electrically isolated from the ground of the HU or the amp. The current seeks the lowest resistance path to ground. If your HU has a bad ground and you amp has a better one, the easiest path is through the RCA. Because of the design of the car's alt there is a small ripple in the voltage that it puts out. This ripple isn't enough to cause radiated noise (see below) but it is enough to be really annoying when introduced directly to the signal.
If I see one more person promulgating the myth that you need to run your RCAs on the other side of the car from the power wire, I'm gonna give them an e-kick to the nuts. Unless you have some really serious problems with your alt, the tiny ripple in the alt's output voltage is not going to cause enough of a current flux to create the expanding and collapsing magnetic field required to induce noise. Also consider that the current flowing through the power wire is proportional to the voltage in the signal cable. In periods of high current there is also the highest voltage in the signal cable and a high voltage signal is less suceptible to induced noise. Factor in the most basic of shielding and you are pretty much talking about induced noise being a non-issue. Finally figure in that if you use a chassis ground, every bit of current that flows throught the power wire also flows through the chassis of the car. Unless you plan on moving the RCA as far away from the chassis as possible as well, there is no point in trying to isolate the RCA from the power wire.