No, it's not supposed to work that way -- all of the windows should move to the top when they are restored. I've noticed this problem myself, but haven't been bothered by it enough to figure out what is going wrong. Although I've seen it quite often, it's not strictly reproducible which makes it harder to debug. I remember when the other windows were made to behave like sub-windows, we had problems with the six windows fighting for focus and had to turn off some of the automatic features. This may be the root of the problem.
Is this a significant problem for you or just a mild annoyance?
Harry