We have heard a few people mentioning this now but have never run into it ourselves while testing so it might be a bit difficult to track down. Are either of you using Steam to launch the game or just the itch launcher? Steam's controller options might interfere with the input.
We have a patch releasing this week that might fix the options not responding, and if it's still broken for you after that we'll try to make it a priority to fix for the next minor patch.