Hi Dorian,
It looks like you'll need to render your GI passes with much higher quality settings, for this scene at least. There might be something about your atmosphere that is casting more variable or contrasted GI onto your landscape, so the simplest solution is to render with higher GI settings.
Try 8/12/8 (Terragen 3 settings, not Terragen 2). This will take a lot longer per pre-pass frame, of course, but, you probably don't need to render every 3rd frame. Every 10th frame might be sufficient. Maybe even every 20th. You could try rendering on 20s, and then only render frames in between if there are problems with the 20s. Rendering sparser GI cache frames also has the advantage of slowing down the rate of the pulsing/fluctuations, which further helps to make the fluctuations less noticeable.
If you still have problems after all that, look at your sky and see if the sky around the sun is abnormally bright - perhaps due to excessive glow factors in the atmosphere or clouds. This is one possible cause of troublesome GI, but I think it's probably still possible to stabilise it using the suggestions I made above, i.e. higher quality GI and more sparse GI frames to reduce the speed of the fluctuations.
Matt