Solved it. It appears to be caused by latest GLES plugin. I have no idea why a graphics plugin is interferring with loading, but after 30 loads.. I can't replicate the error on v0.0.3 of the plugin. If you are that desperate to play Zelda I can upload the old plugin with instructions... but otherwise I'd say wait around for the next release which will invariable fix it.

As for the error it self... it appears to only occur ever on the second run with the same config. Basically I am able to remove the error by running the emulator without a .mupen64plus folder... then replacing it with my one containing a save. Loading it once then not being able to do it again. I'm very tempted to call voodoo magic on this.