I'm having the same problem!! Just got AS 2012 ;yesterday, and right now am not a happy camper. The weather en route does NOT change as the Active Sky map shows. I get constant updated green bars, but it does NOT change FSX to real weather. I may take off someplace with moderate rain, low overcast, etc., fly someplace a hundred miles away, that according to Active Sky should have about the same condtions - but when I arrive it's partially cloudy, no rain, wind almost opposite, etc.. When I check the FSX map view, it's showing what I'm actually experienceing, and where it's getting the data I have no idea - I thought Active Sky was supposed to rule, regardless!!!!
I'll be flying along with rain and lightening, then in a flash it's scattered clouds and picnic weather, even though the Active Sky map is showing all kinds of crap ahead.
I have fuispc, but it has all weather options OFF.