Is there some reason you aren't using the application directly through Oculus? (The oculus version installed through the lobby not just the directx11 version) Instead of installing the app seperately and running it outside oculus?
What you are describing sounds to me like the difference between where you setup your sensors, and a slightly different position where you are actually playing the game from.
For example i setup the sensors at my desk, but i play from the playseat a little ways away...so Aces High splash and cbm always show up way off to the right, but when it launches (the oculus version) it says hit any key to center and i use the fire key on my joystick from my playseat and it centers up and away we go.
As a side note: Some of the perks of using the oculus library version is that it auto updates without you having to do anything and you don't have to select to use the rift, it assumes it. I'm using the beta now which i'm not able to use voice with but otherwise you could just say "Hey Oculus, Launch Aces High" and it would.
So to "Fix" it i'd say you might want to make sure you go through setup with your rift, sitting exactly where you want to fly from AND don't move your sensors.
That should do it.