I am having the same issue in my 2008 Suburban using a Pioneer AVIC-6200NEX unit. The suburban has Bose but no rear DVD entertainment - just rear audio controls. The GM5+ harness is connected to the Pioneer harness through the speaker level connectors (not RCA). There is hissing/feedback/popping from the rear speakers when the rear audio controls are powered on just as JohnArcher described in his post and there is still sound coming from the rear speakers when headphones are plugged into rear controls. The factory controls and head unit still function perfectly as JohnArcher mentioned in his post.
Also, the rear audio controls do not appear to function independently of the source selected for the front speakers. The front and rear source don't appear to be able to be changed independent of one another. If source is pushed on rear controls, it changes the source for both front and rear.
Is there any way to fix these issues? I've tried re-flashing the RR to make sure something wasn't missing but the problems persist.