Thanks Brett - So glad you guys have posted on here, I too am having these issues, but was concerned it was a "why is this only happening to me' situation!
I have attached a screen grab (uuggghh its too early for christmas!).
All the bells are swinging left to right with a script driving the animation, but only when the camera pulls back in z-space does the transparency occur, and only in the render, not ram preview.
I did predict it could be due to all layers being on the same z-depth but i moved them forward by 4 pixels and did another render last night and its still there. My last and only hope is to remove motion blur and see if that helps.
Jeff how did you get on in the end?
"Life's a progress bar"