Has anyone ever seen a case, or a property that would cause the lines between objects to not be drawn during animation? I can see in the console that the operations being called are actually being reached, but the lines just are not appearing on the animated SD.

Is it possible that more than one instance of the class is being created? The default behaviour for Rhapsody animation is to associate the first instance with a class role on a sequence diagram.

Is the animation enabled for the package/classes/operation?
You can check this in the corresponding properties an in the "Advanced" settings dialog for Animation.

Roy