I'm guessing improper technique. I have no idea what your workflow is so I can't help much. Here's a short video showing how to camera track a shot and then add elements to C4D.
Creating something in C4D then extracting the camera is a matter of creating and selecting the right elements in C4D before you run extract in Chinaware.
Thanks for the info!
I ended up doing it the old-fashioned pre-Cineware method — saving an .AEC from C4D then importing into AE which always works perfectly.