It is a known issue, we don't know why does it happen, but we will do something about it, we did what u suggested but only on the title screen (we thought it would be enough), we should do as you suggested and enable the keyboard on the entire game. Thanks!
I think the problem is the Rewired plugin, which has only very limited controller support out of the box.
I'm just guessing, but you may be querying for the presence of any controller, independent of it's actual support; see https://guavaman.com/projects/rewired/docs/SupportedControllers.html#controllers... for more information and how to get reasonable controller support (untested, but this may explain your problem ;-)).