Game ignoring controller inputs?

I used to play PSO2 and NG with a controller but recently it ignores all controller inputs. At first I thought it was the controller that was the problem but it works both in Big Picture mode of steam and on other games-- the problem is with PSO2. Anyone have any fixes?

looks like the controller is in the secundary input, that is mostly a issue with Windows and for some games it won't recognize if it is secundary, you can fix that restarting the drivers but also doing a log off, disconnect the controller then connect again and do a log in.