First of all, thanks for doing that animation. I think it looks good compared to some other Terragen2 animations I have viewed at YouTube. I myself don't do animations and can't help you with flickering (though it seems minimal to me). It seems that Matt of Planetside is the man to see about this. I did a quick search and found this entry by Matt on the subject:
"I have used GI in clouds on a number of real productions recently, involving lots of cloud, and GI flickering has not been a problem. A GI sample quality value of 3 is sometimes good enough. Rarely is more than 5 or 6 needed. It increases render times, but not by a great deal. I know that it probably depends on other factors, and some scenes will be more stubborn.
EDIT: Any time you have a scene that flickers even with high GI settings, please let me take a look.
The main source of flickering that I have found is the cloud layers' Acceleration Caches. I need to set them all to "None" to prevent flickering. This is completely independent of GI though.
I plan to implement GI baking this year."
I hope that helps a little, but like I say, ask the main man (Matt) himself for expert advice.
Regards
John