Big problem that does’t make sense, deck

Take your car to a professional install shop in your area and pay for some help.

Based on your most recent post, you may have a defective HU.  But it's time to get help.

i always approach troubleshooting from a " what's the same..what's different?" attitude... you say both HU's act up in his car, yet not if wired in yours where you snake signal into his amp (say a 20' RCA cable) yet if you install the same HU in his vehicle the problem reoccurs... what the same? the HU      whats different ? the physical power and ground connections (since signal is now going into the amp on car A (his)) applying this same test, does his original HU work fine when "mounted" in your car but plugged into his amp?  if so, whats the same? the HU's... whats different?  the power and ground planes from amp to deck.... it sure sounds like a ground loop or possibly an open ground to me.... keep in mind that until the two components are connected to the same ground potential, it's unlikely you'll experience a ground loop issue.....

also keep in mind that every output stage ( pre-amp and powered ) are isolated.... you could easily have burned ground foils on one pre-out but not the others or a bad OP amp for the sub out which will have no effect on the other preouts.... the problem you were describing sounds like servo noise coming from the mecha control PCB or the pre out section....this is usually indicative of an open ground path within one or more individual circuits within the HU......

a last simple test you may want to make is to take a jumper wire from ground and physically connect it to the shield of the RCAs at the back of the HU... if it's an open ground in the audio path that channel may suddenly "come to life"... you then would have to take the HU apart (i'm not saying YOU should do this) and isolate and repair the burned/open ground foil....

of course it's really tough to try to troubleshoot something from a distance ( over the phone, over the net, etc )

I have actually had a similar issue, at least I think it was similar.

I had my ground come loose on my amp during testing before everything was bolted tight, and the amp grounded through the RCA's of my deck, surpirsingly this was a Pioneer HU that I was using as well.  since a 12 volt ground had passed through my RCAs it fried a nice line in the board of my amp and caused a popping/crackling sound in the deck, when you turn the volume up the crackling gets softer and the subs start to fully respond for short periods of time, but that was just because of the current arcing across the burnt sections of the ciruits which was probably what the crackling and popping was.

I had to replace both my amp and my HU, but as I said this does not sound exactly like the issue you are seeing, but it was a ground issue, and from the sounds of it, it's definetely a ground issue.... but that has already been established.