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What screen resolution and OS are you using? You might be able to fix that by alt-entering and turing on v-sync before going into full screen.

1920x1080 and windows 10.

As long as I don't press apply changes, it works fine. the fullscreen is toggled correctly. But pressing apply changes makes it go black. Game still runs (when I press x, it toggles back to windowed mode) changing vsync didn't help and alt enter works same as toggling.

Even first pressing "apply changes" and then toggling fullscreen on makes it black. Whatever apply changes is doing breaks my full screen.