I can only explain this with a video.
I want the camera to follow the spaceship, but when I attach it, it moves! I could do this in Unity 3, but not in Unity 4!
The Scale of the Ship is 10000 
Unity4 does that annoying proportional Transform if you move it in another GameObject.
Scale your Topmost Object to 1,1,1 and only the !!Model!! you scale to 10000
A better way is if you import the model there is a Importscale option normally set to 0.01 pump it up to 1.