I know this is an ancient thread, but I ran into this problem and I was able to solve it. Thought I should post in case anyone else stumbles across this with the same issue.
It has nothing to do with RCA grounds or the head unit's ground, and the unit itself is not bad. What's going on is a lot of these newer decks have a much higher preout voltage, and that is causing the pop. What you need to do is wire a 4 channel line-output converter to the actual speaker outputs on the unit, then connect the RCA's to that, as it will step the voltage down to a level that works better with these older factory amps.