I don't have a controller, just a mouse, but my laptop does have a trackpoint-style pointer, maybe that's detected as a controller?
Hmm, that makes this all weirder indeed! The controller hint panel should only be visible when there's controller input, but a trackpoint-style pointer should just be regarded as a mouse AFAIK.
Do you see a button in the in-game settings screen that can be toggled to ignore controller input? Does that happen to work?