I feel like maybe messing with your sky texture settings might help? You can get to this by going to options -> display -> sky. mess around with that and see if it helps. May also want to try to screw with environment particles? Just a guess.
Under the advanced options you can also try screwing with turning the various shaders on/off. I can see where one of those may cause an issue like this.
These are all just guesses, I've never had this problem, but they are definitely worth trying.
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