Are you sure that the RCA cables aren't running right next to power wires? AC is always present to some degree in the system. When the RCA cables are near a power wire, they can pick up AC induction and carry that to the amplifier, amplifying the sound.
Try this first if you have not already:
"Noise can be picked up by the RCA patch cables connecting your components. To test this, detach the cables from your amp. (Note: A small number of amplifiers mute themselves when patch cables are removed. To defeat the automatic mute, insert one side (left or right) of a spare patch cable into the amp's left and right input jacks.) Turn on your system and engine. If the noise is gone, reconnect the cables to the amp, and disconnect them from your receiver. If you hear the noise, your patch cables are definitely picking it up. Try re-routing them, taking care to separate them from your power cable by at least 18 inches. Also, newer cars may have a cable that provides power to computers and lights in the rear of the vehicle — make sure that your patch cables aren't too close to this cable."
I assume that you've already done your research, but the article linked below is a good read.
Noise Suppression Guide - Noise Suppression Guide