When trying to enter full screen using f11 key, the compositor thinks things went ok, but you are left with a completely transparent window, upon pressing f11 again your regular sized window is also now completely ruined. Oddly enough if you try for long periods of time it will sometimes work. Race Condition maybe? It does work for other native and wine games, but I have not tried other Java or lwjgl based games. It could be an issue with lwjgl itself. It does however work in xfce, and lxde enviornments.
Related issues
Comments

The issue resides in either the LWJGL libraries, your graphics driver, your desktop manager, or somewhere in between. This is not an issue that Mojang can resolve.