3D layers are all messed up when rendered or played.

Hey,
Have you tried changing the comp renderer to Advanced3D, for the sake of the test? Is the page ofset still present?

Your nested comp (Pre-comp) has problems because you did not collapse transformations. There is no interaction with the default comp camera unless you collapse transformations on a nested comp with 3D layers. 

The workflow is slightly flawed because you do not have a Camera in the main comp or the 3D comp with all the layers. When you turn on Collapse transformations on a 3D layer, the camera and lights in the main comp are used instead of the camera in the nested comp (pre-comp).  If you have a camera and lights in the 3D comp, you must move them (Cut and Paste) or copy them to the Main comp.

Spend some time studying 3D workflows in the User Guide to better understand the workflow.