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There are 2 configs for the joysticks. One for EmulationStation (that’s the es_input.cfg that is created when you first launch RetroPie and it asks you to push up, down, left, right, etc on the white screen) to browse the emulators and the cfg for Retroarch, which is the file that the emulators themselves look to for in-game input parameters. Make sure your retroarch.cfg is properly filled out (go to the configs/all folder and type “nano retroarch.cfg”) with only the buttons you have on the controller– I had a bunch of problems with this as there were more inputs than I had actual buttons so I had to delete quite a few that were not on my controller (using Wii Classic Controller via Mayflash wireless adapter). Hope that helps!