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I am experiencing the same issue. I have installed a fresh 2.3 system and on first set up configured the controller for the emulation staiton, which saves and works fine. I’ve also done the command line set up for the xbox controller to use it for the roms, however I have mixed outcomes. On the NES the buttons will work, but on the SNES and other systems the buttons will only work in certain parts of the game then i can’t go any further because the controller appears to have no effect. I have had a look and cannot find the retroarch.cfg file.
have had a look around but theres a ton of guides all saying different things for different versions of the system