Hey Mate,
Have you by chance tried to use the retropie_setup.sh script to update the binaries of mupen64plus?
I had the same issue as you and racked my brain about what was causing it. It only just hit me that I had to cancel the process for mupen64plus update half way through. Run through that process again using the script above.
e.g.
cd /home/pi/RetroPie-Setup/
sudo ./retropie_setup.sh
from the menu presented:
Select: Source Based Installation
From the list presented use space bar to deselect everything on the list except N64 emulator MUPEN64Plus-RPi
and hit ok with enter
let that run its long course ~1-2 hours
reboot – give it another go