Hmmm, opening EnvSim.act with a hex editor I see some text that describes the process, so that may be it.
"The upcoming weather. If different from CurrentWeather, a transition between the two weather types is made...CloudsTransitionTextureName...The texture used for blending between two different cloud textures...CloudsTilingFactor..." and it goes on like that.
No program I know of to actually edit or make sense out of .act files, so I guess the next thing is to pick one .mis file that loads at start (EastAsiaCampaign.mis, US_NavalBases.mis for example) and see if changing the weather in one of those overrides the default. If it does, then it would be interesting to see if clear with no wind in one .mis file overrides high wind fog heavy rain in another, or vice-versa. Might also be a load order factor, obviously when you start a new patrol in a campaign career there are a whole bunch of different .mis files that have to load.
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