Some fill in on this as I have experienced this as well (last time was last night)...
First time I saw it was when I went to 120hz on my refresh rate ...came up in a windowed "full screen" mode as described above.
Setting it back to 60hz fixed it. Wasn't happy, and kept fiddling with it. Dx9 worked at 120hz, Dx11 did not. Having it open on my second monitor at 60hz worked, having it open on my primary 120hz screen at 120hz did not.
Reinstalled game, stuck back in my settings folder. Worked as advertised.
Went to try 4k again after the updates...so 3840 x 2160 at 60hz. No issues. Wanted to go back to 120hz at 1080p and could not make it work again. Reinstalled, still no workie...removed the video8 fiel, ensured everything was set...still no workie...offset windowed mode overlapping onto second monitor. Removed second monitor, no change.
I'm currently flying at 4k rez, 60hz. Game looks great, but for the big events I would like the extra Horsepower of the card to be able to keep up with all the aircraft...and would like to be at 120hz. Just haven't messed with it again to try to make it work.
Skuzzy, I'm not against use of team viewer if you want to have a go at it.
Dobs