Hi Val - in your test.3dm file I see one solid undeformed object, but I don't see what deformation you are running on it - is there some kind of base curve and target curve that you're using to deform it with Flow or something like that?

But I see you've got some sphere pieces in there - most likely you are running into a bug currently in the deformation engine that it does not process surfaces that have a collapsed down pole point in them such as spheres properly. If you zoom in closely to the pole of a deformed sphere you'll see it looks a little weird in a small area right near the pole point.

I think we actually discussed this a bit previously here? :
http://moi3d.com/forum/index.php?webtag=MOI&msg=4863.1

- Michael