Had the same problem and was able to fix it the very same way. It was devinitely related to All Natural... or at least the AllNatural.esm - made the mistake to only deactivate the files first instead of the whole omod, so I kept getting error massages related to the (deactivated) AllNatural.esm when opening the console. After deactivating the whole omod the weather still didn't change... after I did this thing that Hickory wrote in his first post, however, all went back to normal. How beautiful a clear night sky looks, when you've had only heavy rain storms in the last weeks traveling through tamriel... :o Thank you!