Controller input delay

Im using a wired xbox controller for PC to play. Recently, my game has been having an issue where my player in pro clubs does not respond to the sprint input (RT). When he receives the ball, he becomes stationary, but can pass the ball, just can't move. When I swap the controls from RT to LT, it makes sprint a toggle, where the player is constantly sprinting unless I press RB or RT (protect ball) input, otherwise he will continue sprinting. 

I've checked it's not my controller issue as it works perfectly fine with other games and passes the gamepad test. Ive tried turning V-Sync off and setting refresh rate to 144hz as well. Nothing seems to be working. I also notice that when I decide to use MnK to play, when I go into a Pro Clubs match, only my keyboard is recognised. What is going on?