Did you scale/rotate while in object mode or were you in component mode? Like selecting all vertices then scaling, for example. If so, then that's the problem because while the user might see it as a simple change in scale, Maya recognizes that as the object's actual shape being altered and no longer knows how to alter it's history accurately. You can kind of cheat and make changes to the object's shape, by using a lattice deformer. It'll allow you to indirectly move components around while being able to edit the construction history if desired. Hope that helps!