Issue With Using A Controller

[Transcendence05]

I am using a PS3 controller and software so that it will be read as an Xbox 360 controller and it worked very well for a while but now the game will not read input from the controller unless I am in the pause menu (i.e I can use the left analog stick and the R1/L1 buttons) but then nothing as soon as I exit the menu, I know its not the software because it still works in my other controller supported games and I know its not the specific controller because I've had the same issue with two different controllers, I've also re-downloaded the game and the problem persisted