It might be a Bug, Cliche Suggestion, Uninstall and Re-Install the game.

However, if you're using it, via Bluetooth, try using it with a cord, or try using a Wired-Controller (A Controller with a Cord, attached to it), as I've had a Problem, with an XBox Controller, that was a Wireless one, in RWBY: Grimm Eclipse, where the D-Pad doesn't work, but does, with a Wired Controller.

Anyway, If anything, try using an XBox Controller, if it still doesn't work, try the Uninstall-Re-Install Method.

I Hope this Helps.

I have a worse problem, it doesn't recognize my PS4 and Xbox360 controllers, whether wireless or wired, and the strange thing is that it worked normally before, I don't know if there was an update that ruined that, and it's only with that game because with the others on Steam it works fine.