Alright, so if I want to completely remove eveything and start from scratch, do I just need to do a

rm -R .mupen64plus

and then install it from Extras-devel? I want to start from scratch because I'm still having issues with the proximity sensor not working as the A button when using accelemymote, would I also have to remove accelemymote as well?

As for your previous questions, I was using your latest config files (the one that quits with the q button). It just effected OoT, but I've never tried it before since it was said to run slow. I've tried to reinstalled once. I've deleted the save files and tried runnking it from xterm, with the --nogui command, got to the same point and got the error. The phone was rebooted a few times, didn't change anything.