Please add some info about your system, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.
Are you using RetroPie or just RetroArch ?

@mitu That was it! Thank you so much for taking the time to reply on my thread. The internet needs more people like you.

I've been trying to keep up with the repository the last week or two but for what it's worth I'm on the road again and mostly away from keyboard for most of the next week. It might be that the Thanksgiving holiday is when I get some quality mame2003-plus time again.

Nevermind solved the issue.

No, I mean get in emulationstation get in a game (any game but you have to do this with every emulator)and enter the menu from there with your keyboard. Then you can go to the input settings (with your keyboard) and bind the keys to your controller.

btw: just noticed that RGUI is still the old "text one"; I remember seeing the new RGUI previously (graphical, same as windows retroarch) but cannot remember what core. Lr-mame2003 and 2010 now show the "old" one.
Is RGUI version (new vs old) depending on the specific core ?

@dankcushions said in Better way to change hot key bindings for multiple systems?:

@dinierto that's the correct solution, so i can only guess that there's something in a retroarch.cfg somewhere that's conflicting.

That's my only guess too but I don't know enough about that specific issue

Check the retroarch.cfg files of faulty emulators : https://github.com/retropie/retropie-setup/wiki/retroarch-configuration .

already in the pretty docs too

https://retropie.org.uk/docs/Atari-2600/