Mupen64Plus Configuration Issues

Unfortunately, I can’t configure these controls for the life of me. I’m using the Mupen64Plus core and a third party controller to configure the controls. Therefore, I can’t simply auto-map the controls like you can with a 360 controller. My problem is that whenever I configure the A and B buttons, the configuration is written as “User 1 A Button (C-Right)” and “User 1 B Button (C-Down)”. When I configure my A and B buttons, it also configures both C buttons!

This is a mess! Every time I shoot in Star Fox 64, I simultaneously hit the breaks. Also, when I hit the turbo button, I also shoot a bomb.

I’ve used this core before and never ran into this issue. Do you know how to solve it? The core is unplayable unfortunately with this issue.