Originally Posted by
Packetdancer
Not Square-Enix support, but...
If Steam is causing problems with your controller, it's actually possible to disable Steam's controller-remapping layer (which I would lay 99.9% odds is the cause of any controller-related woe tied to Steam). If you open the Steam 'Big Picture' mode and go to the configuration, you can enable/disable the Playstation controller mapping option and the Xbox controller mapping option.
When they're ON, what Steam does is actually eat the input from the controller, then export a new controller in its place. This allows you to do things like button remapping in the Steam controller interface; you press button A on the real controller, but you've remapped it in Steam to B, so the imaginary controller Steam presents to the system presses 'B' instead, or whatever.
Needless to say, if something goes wrong with controllers, it almost certainly happens in that layer.
Disabling the Playstation or Xbox remappings will make Steam stop grabbing those controllers, so whatever is looking for a controller gets the real one instead of Steam's remapped virtual copy; in most cases, that should fix your problem. (And no, I don't know why the controller remapping setting can -- at least so far as I know -- only be accessed from the settings screen in Big Picture mode.)