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I struggled with the same issue setting up the buttons to be able to navigate in emulationstation until I finally realized it would be much easier to manually edit the cfg file. The file is located at: /home/pi/.emulationstation/es_input.cfg
I uploaded my cfg file here, if anyone wants to try to copy it over theirs
I have the snes30 and nes30, it works for both. I connect my controller in joystick mode, just holding start to turn on.