Ok first of all. USA == NTSC. NTSC is the region that envelopes North American and Japan (although technically NTSC-J I believe), whereas PAL is region for Europe and Australia.

I'm currently stumped... so lets try some exploring. As the game begins loading through xterm... where is it loading the config files from? Try simply deleting .mupen64plus folder and running the emulator.

EDIT: Also I am now officially getting this error.. which is weird as it was working last night. Guess it's become a personal problem I can look in to.