You have nearly the same setup that I have that works very well. First, you MUST MUST MUST disable the camera body's ability to control the lens aperture. The simple solution is no not fully twist the lens in place till it locks. Just twist the lens a tiny bit so that it stays in place but the aperture mechanism does not engage. You will know that this is working when you adjust the f/stop on the lens and the viewfinder preview brightness changes. At this point you need to shoot in full manual mode. I do the following with my D50 and get flicker free stop motion animation.
Also make sure that you run the camera from the AC adapter and not a battery.
Now I have heard that some cameras have worst exposure control than others. I purchased the D50 (now no longer made) because others in the animation world had good luck with it. It was also a 'cheap' camera and could be considered 'disposable' when the shutter wears out.
If your camera has loose control, one possibility to try is to add a small neutral gray target in your animation someplace you can crop it away. You could now use adjust eac frame in a picture editor to get the same brightness from the target.
-Skye Sweeney
FLL Freak Productions
http://www.fll-freak.com
