I'll +1 this discussion, since I've started getting issues with my PS4 controller since updating to 1.3.1.

I played the entire game with this controller, no 3rd party software needed. As mentioned above, I can also use the controller in the Ubisoft Connect overlay (I can even use it on the "Press any button" prompt when starting the game), but I can't it for any gameplay, it just doesn't detect it. I use the included PS4 USB charging cord to connect my controller.

Weird thing is, even if I try to use DS4Windows, it still doesn't detect it. I have no issues with my controller in other games.