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.
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Outlaw Audio Model 976 / 7700 / Ultra-X13
B&W CM9, CM Center, DS3 (side), DM303 (back)
Blue Jeans Cables (XLRs, Canare 4S11 Bi-wire, HDMI)
Tivo Bolt, Xbox Series X, Panasonic ub820, AppleTV 4k, LG C765P
Roon, Allo Digione Signature, Sonore MicroRendu, Uptone Audio LPS-1, Peachtree Audio Nova 150
GIK Acoustics Soffit Bass Traps, 244 Panels, Monster Bass Traps, QRD7 / Polyfusor Diffusers