I'm guessing that the pedals are actually a keyboard with only 3 keys. The OS takes that input and gives it primarily to the program with focus, and to everything else in a different way. That's how OBS can have this option:
You can't stop either of those methods of delivery, but you might be able to tell the other program to not use one or the other, or both, like this option does in OBS.
Or you might change what the other program looks for, or what the "keyboard" sends and change OBS to match, so that the same key doesn't trigger an action in both programs.