Thanks guys, lots to figure out
I wanted to keep the same general look as in the first image but was unable to get it to work with the fill lights, at first.
The first image has a quite golden sun light but the fill light setup has blue or white lights. This caused the strange "under lighting" in the clouds. I eventually changed the fill light colour to the gold (one a little redder, one a little yellower) and this seems to have sorted the problem out.
NO MORE FLICKERS!!!
However I have had to get rid of my smallest 4 fake stones as they started flickering in the distance (Hmm a distance shader might have been better)
I'm rendering 300 exr's now and I'll post the anim when finished
cheers
Richard