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I got about halfway through the game no problem, but now when I boot it up and press the run button on my controller, it brings up the objective marker as if I was pressing the right stick. I have tried reseting the controls in the game, started a new game to see if it was something with my save file and the problem was still there. The PC keyboard controls work correctly for some reason.

I am using a PS4 controller through DS4Windows to make the game think I am using a 360 controller. I don't think that program is the problem since I play steam games with it, and it works no problem.