I've run quite a lot of animations with millions of trees and tight object spacing. Where did the tree objects you're using come from? You might want to try Ben's suggestion of exporting through PoseRay as it can fix a lot of object-related issues.
For general settings to get flicker-free trees, I would use main detail of at least 0.7 (I have made good-looking flicker-free animations at this level), population quality at High or Very High. Other detail settings should matter much less, at least for flicker issues and population quality specifically (e.g. you don't need to be as concerned about atmosphere quality, etc.). As Ben mentioned there is also GI flickering which can occur. Raising the GI Blur Radius to 100-300 should solve this.
You should also make sure there are no alpha problems or other issues with your models. The population system itself works very well and will give good results, provided the source models are setup well for TG2.
- Oshyan