Hi Drueb, I'd trust your own verification of cabling and how it sounds over the auto setup.
I have seen a lot of messages about auto-setup trouble over the years. It can be useful for level, phase, and distance settings but it is a single microphone in a room and can therefore take measurements in a location with a terrible room node or reflection that throws it off.
I agree with your logic, arbitrageur. I figured as much. Thanks for the input.