To clarify a few things, do those squares only appear around objects like trees, players and mobs? Does it look like the skybox is being visible through those squares all around objects (different colors depending on day and if you look up or down)? If yes then I had the same problem and I fixed it by going to options > display > advanced and turn the sky reflection update as low as possible (once per minute) as I noticed that flicker was directly related to the update counter there. Hope that helps.
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