Well, honestly, I think what's happened in some of the installations is that they don't have the pins installed correctly. You have to remove some dummy pins in the 35 pin connector and install the pins from the wiring harness. If a pin is not fully seated, it won't make contact....and believe me, it can be close and not make contact (don't ask me how I know).
I spent several hours on the phone today with the MoCo about this. I was the first person they know of that has tried to install both the iPod and Nav interface. He told me they've had several calls (3) from various Dealers having problems similar to what we've seen here. Part of the problem with the dual install, is there is no real info how to interconnect the units. I looked at it and was able to figure it out correctly, but in the instructions, it says install these pins...if you have the other info, follow that installation procedure. The other procedure says install these pins....if you have....doesn't matter which you start with, you can't install 2 pins into each hole.
The fact that my unit worked perfectly with a RT, and not at all with a Zumo, added to the fact that his RT worked perfectly with his bike (CVO Road Glide Ultra, factory installed options) and did NOT work with the Zumo, I think this is pretty clear.