The only thing I can think to check is that the ground wires in your original radio harness are connected to the audio wiring that goes from the tuner to the amp. In my old 740iL, the two pins for the audio output ground were missing. And, the ground wires for the audio output were tied back in the wiring harness and spliced to the chassis ground. It was done that way at the factory. Here is my post that describes what I found and my fix.

http://www.bimmerboard.com/forums/posts/99394/

Your problem is very unusual, and maybe it is as simple as some missing ground connections in the wiring between the radio and the amp.

__________________
SOLD
2000 E38 750iL Highline Edition, Upgraded with the lastest 2006 X5 Electronics
MKIV Navigation, 16:9 Display, Bluetooth, TV/Video with Backup Camera, Sirius, and Aux Input