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Try this discussion from 2009, hope it points to your solution:
I think it's still a pixel aspect ratio setting. Has surprised me many times.
Message was edited by: bogiesan
One thing that I fogot to mention was that in the final composition I can clear it up by continuously rasterizeing however the 3D moveable camera dissappears when I do so? Any thoughts on that?
You just need to learn how AE works. Without seeing your comp and a flow chart it's very hard to say what is going on but I'm guessing that you have cameras and lights in your pre-comps or your .ai layers in the precomps are not 3D.
If you pre-compose an Illustrator layer and want that layer to be 3D you have to make the layer 3D before you pre-compose then collapse transformations. The cameras and lights must be in the Main comp.