I let auto set-up check my channel assignments for me. Soooo glad I don't have to deal with these issues. Yeesh.
GL, to those who do.
I presume you are referring to AVR auto setup. Regarding channel layout, auto setup simply tells an AVR which of its loudspeaker outputs are connected to loudspeakers.
It's entirely independent of other hardware connected to the AVR. The problem here is in the player.