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I feel so stupid right now. The problem was that I was securing the wiring coming out of the trunk right on top of one of the parking sensors. The moment I moved the cable to the middle of the bumper everything started working.
I have used bike racks and cargo baskets without issue. But the the car refuses to allow AP when the Transporter is attached. I have ordered a raised hitch extension to see if it clears the parking sensors and the error goes away.
Did you ever get any problems with AP not being available after newer updates? I just got the Thule Transporter and my M3LR refuses to let me use AP or cruise while the box is installed.