I am doing a 'morph.' At several intervals of time, there is more geometry in the scene. It simulates things being added.
Each layer is a sequence of stills from Rhino+Bongo+V-Ray and imported into After Effects. Think of it as a short video.
All sequences are from the exact same model. After each sequence is done, I turn on another layer and render the next sequence. You can see the actual frame numbers in Option B. These are absolute tick/frame numbers from Bongo and SHOULD BE the same, regardless of (a) when I start and stop a sequence or (b) which layers are on or off.
This process is actually pretty common to show a scene fade from a wire-frame to a shaded view to a rendered view, all while stuff is moving. I've typically done version A and just made each sequence equal & full length. In After Effects, I then transition (via opacity fade) from the top layers to the bottom layers.
See image with more stuff.
The problem is that frames with the same number should be identical, except with the new layer stuff. They're not. They're from a radically different position. It's like there is tweening happening to each short sequence, when I have turned it off / changed to linear.