[Mark Pyper]

Not sure if this is a solution but I just had this same problem, after effects not displaying layers correctly in 3d space but displaying them in their layer stacking order.

I fixed it by turning off the visibility of all layer styles, not just ones you have activated but the actual eyeball next to the Layer Styles dropdown, even if you have no layer styles activated. I had to do this for each 3d layer and they displayed in their correct order.