It would be helpful to see at least a still frame of the sequence in question to be sure that the problems you describe are what I think they are. But with the settings you describe I think it's very likely you're dealing with changes in the Global Illumination solutions between frames. Your GI settings, if I read it correctly, are very low (1,1,8). As cyphyr mentions, removing GI entirely is the surest way to eliminate that flicker for now, but you may prefer the GI result. In that case you would want to try some higher GI settings, something like 2,6,16. This will increase render time, but you can compensate by lowering atmosphere samples considerably. Unless your scene is particularly dark or high contrast, it's likely you won'd need more than 16 or 32 atmosphere samples, regardless of whether you're using Raytrace Atmosphere (RT). Also I don't think higher jitter than 1 is useful (not certain). I suspect you may have made those settings on the assumption that the atmosphere itself was responsible for the flicker, but it is very likely the GI as I said, especially if the problem persists even with those high atmosphere sample levels.
In the upcoming 2.4 release we will have some features for taking care of GI flicker.
- Oshyan
