@mitu Ok, I think I figured this one out. I added the following line to the retroarch.cfg in the /opt/retropie/configs.hdmi/c64/ folder:

input_player1_select = "nul"

and that seems to have fixed it.

Thanks for your help! It did actually make me start looking at a few other things and pointed me in the correct direction!

Does anyone have any idea why the mapping for the up motion on joystick would be different for player 1 than player 2? This problem only occurs on ultimate mortal kombat. I'm sure the joysticks are wired properly.

Just gonna re image - gonna be quicker :P

@Slugz https://retropie.org.uk/forum/topic/3/read-this-first

in fact, config per core is depreciated in retroarch. it's not in the latest builds so i guess will be gone from later versions of retropie.