It sounds like a screen resolution issue. It probably would be a good idea to go in and set the game to windowed. You can do that by opening settings.dat in a text editor from the RuntimeData folder in the game folder.
Sometimes you get strange interactions between Unity 3D and certain linux drivers in certain circumstances. It's a good chance that future drivers will not have this issue, but for the time being that workaround ought to work. Please do let me know if not.
Hope that helps!