Do you have raytraced unchecked in your atmosphere and clouds? That isn't necessary, since it has something to do with shadows coming from the surface up.
Another thing, you might check around about your settings. Most of these settings don't need to be slammed to get high quality. For example, I use 16 or 32 for most of my atmosphere settings, while I might go a lot higher for the clouds themselves. Another one is the render quality. I never use 1 and usually use .6 for a final render, unless I am making a large render and then I go to .8. But, I'd bet I couldn't tell you the difference by looking at one with a .8 compared to a .6. Another setting is the GI setting. I rarely go over 2. It just isn't necessary from what I can see. Then again, because I don't see it doesn't mean it doesn't matter.
Most of this understanding...well, no...all of the understanding I have about this has come from the support staff and many of the end-users like you and me who come here and share their experimentation, etc. One of the first things we heard about TG2 was the need to be aware that cranking the values to maximum will usually only increase render time and not necessarily make any visible improvements.
Good luck.
