Rift and xbox controller wired.

Hi all. 
I'm hoping some one can help with a frustrating issue. 
I setup my rift with my wired xbox one  controller with no issues. But once I start a game, I. E. Sw squadrons, my controller doesn't respond. Also, if I try and play any other non vr game, I have to quit oculus app, go to task manager and kill all oculus software background tasks before my controller is recognised again. Very frustrating as I have been looking forward to playing Sw squadrons. This isn't a new issue, I just avoid all vr games that require a game controller.
Any help would be great.