Well.... i figured it out. The "problem" is the size of my map.
It is so large that it takes roughly 30 to 40 seconds for the atmosphere to take effect once you change it in GM mode.
The lightprobes are recalculated for the new atmosphere and you can notice it by the sluggishnes of the game as it's calculating the light.
well its time to publish then

I'll have to explain this in the discription.