@wetriner I tried it again too. Didnt get a double entry on the USBGamepad.cfg this time. However when I ran super mario 64 the select button wasnt working again. After checking mupen64plus.cfg I saw it had failed to bind "Joy Mapping Stop" etc again...
No worrys I just enter the values myself, I wanted to understand why 3.7 wasnt auto doing it though yet 3.6 does. Guess I'll never know