I think I would double check the wiring to the mid, does the mid power down at all or does it remain on? I would assume the wire colors at the dash match the wire colors in the rear? Did you cut the wires at the dash or just buy the pigtail and splice in at the rear? If all else fails put it back to stock and see what happens.

My E39 is all aftermarket, Focal utopia component set up front, Hertz Hi-energy coax in the rear. JL 10w6's for sub, currently powered by a JL Jx700-5 being replaced by some JL HD amps. Probably moving the JX amp to the X5 when I begin building a new system for that.