Shooting at different times of day. Usually clouds and sun in the shot. 5 seconds between each shot. Now I could go out and shoot this with a mo pic camera or video camera for that matter: same scenario, use one shot every 5 seconds, and I will not get this same flickering in the density from shot to shot. There is something definately going on with the CMOS sensors. Not an issue if you are just working with stills. But if you are going to string the images together as an animation you need a little consistency from image to image.
It is not just that the sun is peeking out from behind clouds . . . the sun, and the entire image brightens and darkens. I have shot the sun coming from behind the clouds before. The entire image doesn't dramatically change. Yes, the sun gets brighter, but it doesn't have a overwhelming effect on the entire frame.
Maybe Nikon with their older, more mature CCD sensors will be more predictable. I wish I knew for sure.