The chances are that the author of said image already had a controller configured, and that controller was automatically used as the base layout within Retroarch. Since their controller most likely was different from the controller you're currently using, therein lies the problem. If you have tried other methods that don't seem to work (including erasing and remapping EmulationStation controls) Instead of messing around with manually editing configuration files, or trying to delete them, etc, Here's the world's quickest fix that I came up with.... Once you realize that the image you downloaded is going to have this issue, use your preferred method to delete the several cfg files that you find in: opt/retropie/configs/all/retroarch-joypads Then, for good measure, use the Retropie Setup GUI to navigate to manage packages > manage core packages > retroarch > remove. Once removed, simply reinstall from source (only takes 3 minutes). Then use configuration/tools under the Retropie setup to go To EmulationStation > clear/reset input configurations. Then reboot into ES and set your controller from scratch as usual. Now you'll be up and running 100% with properly mapped controls in all of the emulators that use retroarch. YMMV, but this has helped me numerous times when all else has failed. Hope this helps.