Ok I'm gonna do my best to explain this but I am terrible at explaining anything and I don't really understand the problem - So lets say i'm playing in windowed mode, 1280x720 to be precise. Now on my 1920x1080 monitor the EQ window doesn't take up a whole lot of my screen ( the area that isn't EQ, the visable desktop, i will call dead space ) - Now if I fullscreen and try to click anywhere in that dead space it minimizes the game, if that makes sense. So what I do is change my windowed mode to the same resolution as my monitor and then make sure it fills my whole screen and then switch to fullscreen - now that dead space is gone and clicking doesn't cause any problems.
I can't word that any better at the moment lol But maybe try that, change your windowed mode resolution, make sure it takes up your whole screen, and then go fullscreen.
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