The M Audio with the 10 in. subs is unique to the M5. The base audio with the Nokia sub unit is an upgrade in all other e39s. I had that system in a 540i and know that the signals can be tapped to add an amp and better subs. I think the Nav unit adds to the complexity of the signals between the head unit and trunk mounted equipment. Has the installer tried reverting back to stock to see if it works? Hopefully nothing blew. Good luck.
Isnt there a fellow board memeber somewhere in TX I think who has his own audio shop, maybe he would know, I think I remember going to his website and looking at his car during a tint thread, and I thought he had a custom stereo setup, Josh