I have a problem with mine, but I know what it is. It may help you.

I hadn't seen any wiring harnesses available when I did my install, so I took some RCA cables and spliced them into the factory wiring. Right now I get some alternator whine intermittently, but I know it is from the RCA grounds. On the wiring from the factory harness back to the Bose amp, all 4 channels share a common ground. I only have problems because the job I did sucked (I now have one of those nice harnesses on order from caraudiosecurity.com). Perhaps your problem may be related to the shared ground? Of course this is in a 99 A6, so YMMV.