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Yes jstest shows select as 6 and 7 as start. When I start a game this is the text I see in yellow:
Joypad port #0 (SFC/USB Pad) configured
When I ran the joystick setup from the setup script it said it wrote USB_2-axis_8-button_gamepad.cfg, but I’ve also tried changing USB_Gamepad.cfg and it doesn’t seem to fix it either.
Correcting the keys in /opt/retropie/emulators/pisnes/snes9x.cfg did fix that emulator so I’m assuming it’s a misconfig but I can’t tell what file it’s loading from the text it prints.
Could it be a problem with auto-config? I can’t seem to find a similar config to snes9x.cfg for all the libretro ones.