I have had this issue with Project Cars, which I have now labeled the worse VR experience on the Rift. I can only recommend uninstalling the game, if it is just one game, or running through your oculus startup again.
I'm having the same problem. I've never played E:D and am excited about it but fuck my life if E:D isn't the worst new user experience I've had.
Before the XB1 controller problem (after the recent update?) I had to solve the minigame of how to select a new player name. If any of you started E:D for the first time from Oculus Home, you know what I'm talking about.
It's August and having a similar problem. I have selected controller as the default input scheme but can't get it to pick up any inputs at all other than the start button and d-pad (when in menus).