Something I have noticed when I add a planet (either the generic variety or one of my own creation) is that when I reposition it in the sky, its atmosphere stays at the original location. If I put Sunlight behind it, it completely blocks it out like an eclipse. The only way I've found to correct this is to go to the planet's internal network and disconnect the atmo, then level up and move the planet, then go back in and reconnect the atmo. I know Terragen 2 didn't have this issue. Not sure about T3 - I skipped over that version.
Anyone have this happen or know of a fix?