Are you using the newest one from the play store? It's a different developer now so the name changed. I think that was the problem for me. Everything works fine now though with the change that I made
I couldn't for the life of me find this on any of the forums or anywhere on the web so I had to do some playing around to figure it out but for the newest Mupen64Plus on the Nvidia Shield by FZurita is this setting
Mupen64Plus AE
Google play Nvidia Shield TV
exe=org.mupen64plusae.v3.fzurita/paulscode.android.mupen64plusae.SplashActivity
parameters=
I can't for the life of me get the retroarch core to work for me so hopefully this helps someone out also