@dwfmba same problem here. Gpi case 2, recalbox 9.1.
When docked, all my controllers (usb wired and with 8bitdo dongle) works while in menu but when launching a game, it doesnt work, like the gpi case built in controller was going back as player one i guess.
Sometimes it works but the mapping is weird.
Hope there is a solution.
Regards.