When I move md3s around, like Raven's claw, or a shuttle, I did it by making a func static out of an origin and a tiny piece of NODRAW brush. Then I put in the model as model2 (key). This have the negative effect of not seeing the model in editor, only in the game, but it's not such a big deal. Anyway, to move any model, it must be an entity (or a part of an entity) also in the game.
I cannot, however, offer any guess to your difficulties concerning the lack of analogous behavior of models. It's something I haven't myself noticed. Are you sure you didn't do something with the Editing tools installations between the use of the models in these two maps?