This bug suddenly showed up today after me having no real problems besides a few crashes on startup. When I launch the game and I am in one of the menues, be it the main menu, battle or fleet menu, the game suddenly minimizes. If I go back into the game it does the same after sometimes 1 second or 30 seconds. It does not matter if I click somewhere or not. I haven't been able to launch a battle so far because of this so I can't say if the same would happen during a match.
I was able to fix this by changing the screen setting from Fullscreen to Borderless Windowed. Since then it did not happen again. It might have something to do with me running a dual monitor setup.