I've had similar issues though usually it's because another window or app is opening/maximising on the same screen I'm running FFXIV on - though usually I can click on the FFXIV window and it sorts itself out. Could be driver related? Have you updated your graphics drivers recently?

If you ever get really stuck you can set display options via editing the config file located (by default) in \Documents\My Games\FINAL FANTASY XIV - A Realm Reborn - look for FFXIV.cfg, open it with Notepad and you can then set system options accordingly such as resolution, fullscreen mode, display, etc.

Recommend making a copy of the file before you edit it as a backup and don't mess with it while the game is running.