Ground loop-engine whine in rear speakers. Help me please!?

[Josh M]

Ok i think that i have tried every trick in the book. I have a pioneer deh-4000 Head Unit. I have stock front speakers and 6x9 infinity 3 way speakers in the rear. I have two 12" subs in the trunk. The subs are powered by a 2 channel amp. The rear speakers are currently powered by my other 4 channel amp, while the front speakers are powered by the deck. My problem is that when my rear speakers are connected they make an annoying whining sound. This only happens when the car is started or when the ignition is set to the on position right before starting. The sound does not occur when i have the ignition turned back. The sound get higher pitched when i rev the engine. There is also a sort of noise when i switch between inputs such as radio, cd and ipod connection. When i play a cd i can almost hear it reading and a noise when changing tracks. Again that only happens when the car is started or the ignition is turned to on. I have the RCA cables run separate from the power cable. My grounds to my amps in the trunk are solid and sanded down to bare metal. I have tried different positions throughout the trunk and it makes no difference. I also have a different ground from the factory one running from the harness to bare metal on the floor. If i unplug the RCA cables from the amp powering the rear speakers the noise goes away. I have also tried different RCA cables to see if those were the problem which they are not. I have also tried a different amp to see if that was the problem which it was not. The only thing i have yet to try is a different brand of deck to see if that is the problem. If that isn't it are there any suggestions? I have looked through many forums to try to find an answer but cant find anything. Any help would be appreciated.