Hmmm. That's a good point, and it's stupidly obvious, I don't know why I didn't to try to fix it before. I'm gonna try to redo it and see if anything changes. Thanks for the help so far, by the way.
Most of the meshes and textures are stored in Fallout bsa 's. I doubt that's where the problem is though. There are several sky replacers, starry nights, enb's, weather mods that muck with the sky. If you've added one of those, that's where the problem lies most likely.
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EDIT: Nevermind, it fixed it for all of 2 minutes, and now the problem persists. Pavement ahoy.