If you're hearing it on other sources, then it's not the ipod channel issue..
Look hard at any amp and or speaker wiring..
Zero problems with my factory nav unit... It is in an '05 Escalade. I used the Metra adapter, and of course sound is output from the F90BT to the factory Bose amp. Again, never had this problem until the install, which leads me to believe it is either the harness or the Pioneer. And since others have reported similar problems with the head unit, it points me in that direction.