I think you're right. I'll have to go back a few saves and pull out the Atmosphere and Cloud Density settings.
I ran into another problem. I found there was obvious banding on the animation as the sun elevated. It's not obvious on a still, so have supplied a link to a .mov file zipped. This is not the final movement, I wanted to see how the sun level interacted with the clouds as it moved, especially in the red side of things.
www.mediastation.co.uk/AnimationIssuesTest01.zip
After rendering out a cropped area with higher quality settings, found out this wasn't the problem. Then I switched off my 2D cirrus layer and rendered another strip out, which seems to have solved it. Looks like there is no 'fall off' with the light on that layer. I'll render out another pass this evening. I may have to comp the cirrus layer in post with a moving mask. Not a biggy.
I've also up loaded frame 68 out of 100 to highlight the problem, which isn't that obvious unless you see the animation.