@lucklocky
mupen64plus was broken in retropie sd card image 3.1. Reinstall (binary or source).

@saucy
I think you do not pass all necessary parameters.
Example:
mupen64plus –noosd –fullscreen –gfx mupen64plus-video-n64.so –configdir /opt/retropie/configs/n64 –datadir /opt/retropie/configs/n64 %ROM%”

Please take a look here:
https://github.com/RetroPie/RetroPie-Setup/blob/master/scriptmodules/emulators/mupen64plus.sh#L170