The problem here is that it is trying to set the game to a resolution that does not match your desktop, or something on that order, and it has offset the buttons because of a strangeness with how that works. The game is functioning, but you have to click in magic invisible areas to hit the buttons that are way elsewhere in actual visual coordinates. It's something to do with how linux handles fullscreen mode on certain machines, it's very odd.
To fix this, go into settings.dat in your runtimedata folder inside the game folder, and you can change the settings for things like windowed mode, the resolutions in question, etc. Once you get a good match set up, things will line up properly and no worries.
Sorry for the confusion there!