Ah, okay. If that’s the case, then I bet the management software is confusing input mapping. Rather, I’m assuming the management software gets in between the keyboard input, and what proton wants to see. If all other inputs work fine, then it’s the management software with a pesudo-device that is causing the issue.
So it sounds specifically like what I said above, and disabling the analog functions puts everything back to normal working order. So, I guess check with their support folks to find a workaround. I’m sure they have one with proton startup flags or something.