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Why is this happening?

Are you using the metro interface? I've never seen icons packed into such oddly spaced boxes.

Try setting a different wallpaper or just setting a background color without wallpaper, and see if it happens again.

Running your game in borderless windowed mode should prevent this problem from occuring, because the desktop will always be rendered in the background and not succumb to redraw errors.
 

It's a software called Fences, it helps you make your desktop abit more nice.
About chaning the wallpaper: I know how to solve it (just changing to a different desktop background), I wanna know why it's happening and how to prevent it from happening in the future.

I'll try to uninstall fences and see if it happens again.
If anybody else encountered this problem in the past, I'd be happy if you could share.