I can confirm. After playing with settings, copying new versions of retroarch into my portable folder/etc -- IF you have 'AUTO SAVE STATE' and 'AUTO LOAD STATE' turned to ON in the saving options, Mupen64plus will not work.
I couldn't figure out, for the life of me, why Mupen wasn't working. After several hours of playing with settings, I am able to reproduce the issue each time by turning on the 'auto save states' option.
Thanks again for the help, Lordmonkus!