I was working in Unity preparing to have some fun with the Touch controllers when they arrive. I'm using the Xbox one controller as a stand in while I wait. Previously I had plugged the controller in by a micro USB cable, but I recently got some fresh batteries, so I unplugged it and put them in. I could not for the life of me get the controller to connect properly. It would flash, connect, then immediately turn off. After hours of googling I decided to restart my computer, which did actually fix the problem. In a programming session I decided to turn the controller off while I was working to save on battery, but when I turned it back on it had the same problem all over again. I figured it must be one of the apps I was using preventing it from connecting, and after some trial and error I sussed out that the culprit was in fact the Oculus App.
TLDR: If the Xbox one controller shipped with the Oculus Rift is
disconnected from the computer while the Oculus App is running, the app
will automatically disconnect the controller every time you try to
reconnect it from there on out until the app is restarted.