I don't use wind, so, I don't modify anything to do with weather. I would watch out for the horizon fix, lightning/thunder as well. I did notice the fogColor value change when using the weather, but that could be insignificant.
OrbyxP, I just now noticed this. The fogcolor changes are part of my cloud mod that helps match the horizon color with the skybox color and the specific cloud type in my cloud mod. If you don't use the weather manager, you won't be seeing the clouds quite how I designed them to look.