Never happened to me, though i will admit, i usualy only hop in VR once i click the Fly Now button, i personally never found any interest of prep my flight and wait loading screen while being in VR mode, so when ever i load a flight plan in the world map, i simply do this in normal 2D screen mode, load the game, press button Fly Now and then tujrn VR on, put my headset on and center my view. But this is my own preference. Only when in game and ready to fly do i press my Swap to VR keybinding.