Hello!
I know that on steam link all controllers will stop working if you disable XInput, however, this shouldn't affect your game when you aren't using steam link. That said, I actually noticed the same issue you described happening to me too in the currently available build of the game, but also thought it might be a one-off. The version I'm running with locally (a version that will be released this week) does NOT have this issue since it has a newer version of the controller library we use, so hopefully this will be resolved for you as well!
Brett