First thing to check: mixing 2D & 3D layers in the same comp. You won;t get the results you expect.
I've had mixed results. Sometimes it works as intended, 2 and 3D working together. Other times AE doesn't bother showing 3D layers. Is there some sort of successful formula I should follow?
Are you using the ray-traced renderer or the standard renderer?
Are your layers set as guide layers?
Are you looking through the Active Camera in the composition that has the 3d layers?
Have you set any of the comps to collapse transformations/continuously rasterize?
Also, what exact version number of AE are you using (down to the last decimal point)?
No Guide layers in any comps
Looking through a V-ray Camera (imported via Compositor Link)
I haven't collapsed any transforms or set anything to continuously rasterize, I don't' know where those features are.
AE version: 184.108.40.206
Is there a reason you haven't updated to 13.1.1? It fixes a lot of bugs.