Hey, i had this Problem only for n64. I tried some different Roms and it seems to work for me now. It was simply related to the Roms i used in my case.

Hello all, I've got some brand new FC30 pro controller for my Recalbox (pi3). I connected them via bluetooth and the configuration of the controllers was pretty easy via the Recalbox OS. Ive got no problems with playing psx games and others, but for some reason my controllers doesnt work at all, when I try to start a n64 game. I can start it from the menu, but as soon as the game starts, my controller is out of function. (yesterday i was able to get out of the game with the non working controller for some reason (hot key (select) + start). I'm pretty new to all that, but I searched quite a lot on the web, without finding the right solution for this problem. Did anyone have the same issue with these controller or knows something about it?   please help,   thanks