We were able to debug the issue and apparently it was a bug related with the way we were building the game in Unity. The problem was posted to Unity's issue tracker and it will probably be fixed before we launch the final version of the game.
For now, we built the game using Mono and everything seems to be working! The game was being tested inside the Unity Editor before and this is why the gamepads seemed to be working. This time, the final build was fully tested and hopefully it will work for you too :)