I tried using my keyboard with my controller disconnected from my PC, I tried using my controller (which is a PS4 controller) with and without DS4 Windows active and nothing works. In Mario 64 for example I am unable to press the start button. I know that my controller works though because I works with every other core and on steam, so it’s a problem with this core in particular. I remember that there was a core called Mupen64Plus (no -Next) and everything worked there, but it is no longer an option in the core updater to get that version of Mupen.
As a quick update if anybody comes across this, I figured out the issue, at least to a point. I was running a hacked version of Super Mario 64 that made the game run at 60fps, if I run an original rom it works perfectly fine. I do find it odd though that the hacked rom does not detect any input at all.