im looking voer one of my previous levels at my atmosphere triggers, I have one 2 atmosphere triggers, both are not set to global. in the trigger type: atmosphere section of the SideBox, I have the atmosphere named, and no GUID.

also I dont think it makes much of a difference, but i also set my physics type to polygon for my atm-triggers and bumped their height waaaaaay up (100)

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I hope this is what you mean, my previous comment was addressing what I thought you were looking for more function over your day/night cycle script (which I think is cool)