I was unfortunate enough to have to reinstall Win10 and since then FO is stuck in windowed mode. Or I don't know what exactly... I can switch between windowed and not windowed mode in the options menu but no matter what, if I use lower resolution than my desktop (and because of text scaling I want to) the game just appears like a window in the middle of the screen. Not only the menu but during the actual game as well
I have Windows 7 and Linux Mint, but try this. Open your FleetOps file, then enter to OPTIONS-------->Graphics Settings, and there you can check Window Mode. It's a suggestion, nothing else.