I get those weird popups when I'm in one of those two modes mainly in the menus, but also in game.
The only thing that fixes it is when I put on windowed mode but that is not what I like as that forces the game to run at my native desktop resolution and I wanna play in 640x480 just as the devs intended.
How to fix this issue?
V-Sync doesn't change a thing. None of the in-game options do.