I decided that it would be neat to create a ship where the engines were not attached by superstructure, but instead were attached to the ship by glowing energy. So I built some engines and put glows underneath.
When all of these are separate, it looks right in the module screen.
However, if I make all of the components of the engine structure and make them a composite, it works fine initially on the design screen. But when I flip to the module screen, the composite is broken and they all move to the a single spot.
When you move back to the visuals screen, then it is obvious that all of the individual components were split up and all put at the same spot.