hmm I know that in custom battles, you can't choose the weather with the maps that have the little X next to them, make sure you try different maps, if it doesn't work still I'm sure it has somthing to do with descr_geography_new which is the file I modified to tell the game to use different overlay textures for specific climates. I'm sure that the changes I made to it should not effect the weather at all. try playing on different maps and see if that works, let me know if you figure it out or get any results.