Hi Stustaff,
The game must be run in some form of windowed mode in order the gamepad to overlay properly. I should mention that the gamepad is the least developed and "most beta" of all the new features we've added. I think it needs quite a bit of work and honestly will probably take back seat to a number of different features for a while.
We have some exciting plans for the gamepad though, hopefully it will meet those expectations sooner than later.