I think it's overriding the button config of the N64 controller. The most convenient way for me would be to get a second USB N64 controller.

@polygaryd you were replying to a reply from 2 years ago, from a thread originally started back in 2016. it's not helpful to bump ancient topics because they can contain a lot of outdated/wrong/irrelevant advice. if you have an issue please post a new thread.

@hannaman some ports require manual configuration. Most things are documented on the wiki - see https://github.com/retropie/retropie-setup/wiki/First-Installation for a fresh install.

I recommend doing that, as I have no idea what state you have bought the software in.

"Note for eBay: No copyright material is contained on this item. All software supplied is open source and free of copyright. " Yeah - sure!

I ended up just building it from scratch. I tried what you said. After one of the reboots it started saying my es_systems.cfg was messed up and had to fixed manually. I used the bak that was there and that did nothing. Its no big deal. Its always been an ongoing project

Coincidentally I have purchased and tested a cheap USB hub with 7 ports on my raspi1 today. Some ports doesn't work as expected, but I didn't have time to check it deeper.

Did you turn on the "Save config on exit" in RetroArch (config_save_on_exit = "true" in retroarch.cfg). I'm not sure but by your description it seems to be your problem (at least one of them).

BTW, maybe you like to know this tool: https://retropie.org.uk/forum/topic/1167/here-is-a-way-to-select-joystick-for-players-1-4-global-or-emu-specific