I've already asked other people and looked all over and I can't find anyone else having this problem. And I don't have this problem on any other games.
I already tried verifying the games cache (although I knew that wouldn't work). I think it's caused by ShadowPlay because the squares are where the ShadowPlay status indicator and webcam overlays go.
However, disabling ShadowPlay doesn't fix it and neither does disabling the overlays inside ShadowPlay.
Here is a picture of the problem:
If I alt-tab and then go back in, they're gone for a second and then they show back up again.
They stay there the whole time and never move or flicker how do I get rid of them??
I know this isn't a question about the game and doesn't really belong here but I had no idea where else to ask that I might receive an answer.