Apparently it was a problem with the .bak file for my controller located at /opt/configs/all/retroarch-joypads/. Deleting it solved the whole situation. I noticed that the script module is configured to ignore it, but I thought it might not be for some reason and sure enough it paid off. A new .bak has even been created and is not throwing Mupen64plus off, so I assume it was a fluke of some kind.
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