I would suggest either h.sie's hardcode fix and/or Stiebler's add on for the same mod. H.sie's mod runs a whole new weather mod, Stiebler's add on just fixes the stock SH3 weather, which, as you have experienced, is broken.
I would suggest that you use more than the weather fix in those mods, as there are tons of other goodies floating around in there that make it a "must have" for me.
Good luck!