To avoid these problems is exactly why the figures have to share the same OBJ file. I've used MM4 to copy morphs from one figure to another, and have experienced no problems whatsoever, every cr2 that I've used it with works perfectly fine, and all morphs work as they should, the only beef I got with it is that it copies the morphs reverse order, and that makes a specific morph a little hard to find.

Ask me a question, and I'll give you an answer.