We had a similar report a while ago on a Linux as well, menus take input from keyboard and all controllers connected (in that report it was a steering wheel constantly moving downwards). If you can think of anything connected that might be causing this issue, unplug it and try (and tell us what it was!). Otherwise I have no clue what could be.
Sorry for the inconvenience and we are happy to see that you were at least able to play the game!