Ok, I used SH3 Weather with GWX2.0. I set up the weather "manually" at the start of the patrol with some rain, clouds overcast and bad visibility to cut with the everlasting "Clouds partial, Visibility modrate, wind 4ms" nice weather pattern

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Well, first of all, the 2 109s overhead in poor visibility conditions does not make sense. Moreover, when loading a saved game (far from base, of course) "precipitations none" becomes invariably "precipitations medium" and the rain disappears after a few secs leaving you only with the sound of the rain...without the graphics...
What I'll do now is to try to run SH3 Weather without the manual option to check how it goes
I will keep you posted about this new set up.