@Bradyadams
Which configure file? The mupen configure "mupen64plus.cfg" or the autoconfig file "InputAutoCfg.ini"? I recently ran into same / similar. No matter how much I edited the mupen config controller sections no changes. Even if I set the controller to manual config but no luck. The global buttons like escape I could changes.
I then found an old auto config file that had info for keyboard already setup. I copied this into the config folder and was good to go. Reading the wiki it made it sound like the auto config should be generated when you first start retropie, but I am guessing if you only config keyboard it might not.
