This is what RetroLink and Retro-Bit N64 USB adapters do, because they don't adhere to the USB HID standard.

I posted a couple of possible userspace drivers here https://www.reddit.com/r/RetroPie/comments/53bt1d/retrobit_aka_retrolink_usb_adapter_driver/ but nobody has reported trying them out yet.

Alternately, get a different adapter. I have had success with one which looks like this: http://i.imgur.com/cC8iegW.jpg

okay, so i went inside and removed the USB hub and tried running straight to the adapter to the zero and still get the same issue. Controller vibrates and no lights.

@jrmymllr yes, it remembers. at least, for all the lr-emulators, and emulationstation itself.

@meleu Yep, changed it, but it still wants to use controller #1 to control Luigi

@5paceCat I recommend the 8-bitdo as well. They work great.

I'm having the same issue with Teensy LC. The symptoms are exactly like https://retropie.org.uk/forum/topic/3860/usb-joypad-teensy-appearing-as-2-joysticks/3. Were you ever able to find a solution?

The problem if i recall correctly is that the second player is player 1 in that game. Some emulators fixed it but some didnt.