The global illumination looks to me to be the problem, but I don't think turning it off is a viable solution. Because the scene would be shaded incorrectly.

Try increasing the GI sampling quality, but lowering the relative detail. Maybe so the render time is the same as before.
(eg relative detail 2, sample quality 18)
My hunch is this should lower the flicker but decrease the amount of details in the GI, which you don't really need.
I only have the free version and I haven't done any animation tests. So anyone feel free to correct me.
Motion blur is on isn't it?
Edit: also you don't need raytraced shadows for the clouds in this scene. If I remember correctly they only affect the atmosphere being shadowed by the ground. And the clouds are above the ground