I have this resolved after a bit of tinkering.
I had a old controller config in the mupen64 cfg file, I told it plugged=false.
Then I manually edited the config to match the buttons, using the same config you just linked to above.

this old post on the old forum helped too.
http://blog.petrockblock.com/forums/topic/8bitdo-nes30-pro-hotkey-problems-in-mupen64plus/

Thanks everyone.