I’m having the same issue with the Buffer Underrun errors, but getting (0), (1) and (2). The system works, buttons are mapped correctly, just no audio.

I am running audio through this USB device (http://www.adafruit.com/products/1475) using this tutorial (https://learn.adafruit.com/usb-audio-cards-with-a-raspberry-pi/updating-alsa-config) without issue on everything except for Mupen64Plus.

My guess is that the OUTPUT_PORT setting in mupen64plus.cfg is trying to send the audio through either the HDMI or the 3.5mm jack and not through the USB.