I have the exact same problem where I exit MSFS 2020 by selecting “Quit to Desktop”, the MSFS window disappears and then the software hangs with the taskbar button stuck at the “Are you sure you want to exit Flight Simulator” popup. The CPU for that task is about 50%. This problems occurs on a brand new computer immediately after a brand-new installation of MSFS2020 and NO add-ons (3rd party or otherwise).
Anyone have any clue???