Controller Help

[Darud3]

I played Melee with a Gamecube controller months back and it worked fine. I was playing some Unity-based games and found that VJoy, which I now know isn't the best to download, breaks Unity mouse controls. I uninstalled it for those games. I recently dumped my copy of Xenoblade Chronicles onto my PC and I'm trying to use both an Xbox One controller and a Gamecube controller on it with no luck. I went through the process of using Zadig and reinstalling the driver, and Dolphin recognizes both controllers. Xbone controller was able to have its buttons bound via the "default controller" option as well. Ingame, neither are picked up. Is Xenoblade Chronicles simply not compatible with these controllers, or am I doing something wrong? I'm on the latest version of Dolphin as well, 5.0-10121. Any help is highly appreciated.