Ok, so theres some things to concider. Weather zones aren't just brushes but also entities. Depending on how you added those, it might not work like that. Second, weather zones are not mandatory to make inside or outside brushes work correctly. Weather zones are just used to speed up the loading of the inside/outside info. IF you have weather zones, inside or outside brushes that are NOT inside of a weather zone are ignored. Jedi Outcast only had outside brushes, Jedi Academy added inside brushes. Only one type of those brushes are allowed per map. So if you mix inside and outside brushes, the game won't load the map. Reloading a map might break the cached weather info, maybe a bug in JA:Enhanced. This needs some investigation.