I Got the same problem. I use the Analoge Jack for sound instead of the HDMI.
I solved my problem with the following steps:
If you open the next file “mupen64plus.cfg” with command:
sudo nano /opt/retropie/configs/n64/mupen64plus.cfg
Then you will see the next piece of code somewhere in the top of the file:
# Audio output to go to (0) Analogue jack, (1) HDMI OUTPUT_PORT = 1
I just changed the “1” to a “0” and rebooted the system.
Maybe this helps for you.