Did you noticed that game changes the file to the default values each time you start a game and each time you start a new battle (at least it does it for me)? I'm talking about MTW/VI 2.01 version. As I said before I can prevent this by changing file attributes to "read only" but it really doesn't matter. I've tried several quick battles, custom battles and campaign battles and weather looks pretty random ("fine through the day" mostly).
Gollum, which version of the MTW do you have? Original, gold, eras?