This is a known issue (it was posted on reddit), and the way you fix it is by doing this:
Do this only after the game has reached the main menu:
Download Process Lasso, right click FlightSimulator.exe in the process list, go to Priority Class > Current and disable “Windows dynamic thread priority boosts enabled (*)”
It should look like this:
This should make the performance as good as when you click off the game’s screen.