hmm, weird! are you trying to play with controller or with mouse? if mouse, disconnecting the controller would maybe fix it? if controller, don't move the mouse? it is by design that small UI windows disappear when you switch input devices and it sounds like that's happening for you all the time.
I also gotta mention that I don't actually own a linux computer and can't support every linux setup; I just export Hidden Folks to Linus from Unity and it seems to work for 95% of people. I hope you're not in that 5% camp!