I used to get horrible ignition whine on my HU, especially with the AUX selected when there was nothing plugged into it. I also noticed that when the unit was running and I touched the RCA inputs for AUX the noise got MUCH worse. I then reinstalled another HU under the Rio using the AUX input jacks...and the noise totally disappeared!!

In summary, I would suspect that the AUX imput jacks are not grounded and are thus picking up some kind of electrical noise, which is then coming out through your system. I would recommend that you try to ground them if you can!

Ed