Hi macca82.
I experienced something similar to what you describe.
If you are already in MSFS and when changing to VR mode you find yourself in the oculus store, look down for the oculus control panel thing (console?) and you should see an icon with a set of black and white lines on the panel (Mine was between the “Home” and “Virtual Desktop” icons. Click this and it puts you in the cockpit in the sim.
Unfortunately sometimes it unceremoniously dumps you on the floor of the cockpit jammed up against the rudder pedals, or even facing backwards 
…
This is where the next important task comes in… Binding the re-centre view in VR key. Do this BEFORE you even try getting in VR mode. That way, you can re-orient yourself immediately when you enter the VR mode.
Good luck! It is worth it! The Rift is working much better than I thought it would after rolling back Nvidia drivers and tweaking the settings a bit.