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I would think it's that you've got overwritten changes. Maybe making a bashed patch (with wrye bash) will work? I don't use those mods, and I haven't touched Skyrim in ages, so that's just a wild guess.

I suppose you waited three days for the weather to change, yes? IIRC it takes about that long for weather mods to take effect. If you did, my best idea would be to load all your weather mods in TES5Edit and look what conflicts with what.