In my case i edited both the InputAutoCfg.ini and the mupen64plus.cfg (in /home/pi/RetroPie/.config/mupen64plus or /home/pi/.config/mupen64plus cant remember). I just added my own specific joypad name.
When you say you “added your own specific joypad name” does this mean you added a name of your choosing or is there some way to get the name of the joypad from mupen64plus output when it is starting? I have read that you can register your control but don’t think I’ve done that – is this how you get the name of the controller?
Will be looking into this later today – gotta be honest – this whole configure joysticks thing confuses the hell out of me but I’ll do some trial and error.
I’ll see how I go and hope that in the meantime you can answer my couple of questions here and/or someone else may come along and shed some more light on this for me.