I'm not sure how it started happening, but I've since removed Natural Weather, and tried other weather mods to see if that fixes it, but I'm still stuck in this weird rapidly appearing on/off dense fog weather. I use Streamline, is that the culprit? I've been using that for awhile, and only today did the weather freak out. I've tried playing with that disabled anyways.
I could actually go with just having no fog in the weather, it makes my SSAO look bad anyways. I'm using one of the settings in the OBGE thread, it looks fantastic- I can't not use it even if the fog makes it look odd.