Here is the new mupen64-0.1.ebuild and the mupen64 "wrapper". It is working for me.
Created attachment 13521 [details] (update) mupen64-0.1.ebuild
Created attachment 13523 [details] (update) files/mupen64 This is the new "wrapper" script.
I believe this is already in portage. Reopen if the current setup for mupen64 doesn't work for you Fernando.