@amplifuzz did you try and remap or check the mapping in the Retroarch menu?

Pull up the menu depending on your controller but SNES style controllers is select+X. Then Quick Menu - controls - input section. See if you can remap it there or change the mapping to fit your controller.

Also...remember C64 games also have joystick port settings to switch. But sound like uiu already have that covered.

I did it this way:

copy the default RA-controller-config to another place of your choice (i.e.: "/home/AMIBERRY Inputs/") edit the button-mapping as you like in this copied file start AMIBERRY-GUI go to "paths", navigate the "inputs"-path to your new one. click on the button "rescan paths" There you go, the inputs are now as you like to have them global for all games ;)