Hi.
I have the same problem.
After checking mupen64plus.sh, I found that every time when I run this file, it would regenerate mupen64plus.cfg.
You could find this :
# write hotkey to mupen64plus.cfg
iniConfig " = " "\"" "$configdir/n64/mupen64plus.cfg"
iniSet "${hotkeys_m64p[$i]}" "$bind"
To solve this problem, I just edit mupen64plus.sh,
# write hotkey to mupen64plus.cfg
# iniConfig " = " "\"" "$configdir/n64/mupen64plus.cfg"
# iniSet "${hotkeys_m64p[$i]}" "$bind"