This happens 100% of the time.
If I hold Alt-Tab (to switch between applications), I always see two copies of the application. One of the windows allows you to select the normal menus at the top of the screen, the other doesn't. I happen to have two monitors, but it behaves this way regardless of if I configure to use that second monitor.
When I start up X-Plane 11 each time, it starts me on a black window. It works to Alt-Tab and select the other window.
I have Windows 10, and a GeForce 1060. Nothing exotic at all.