The issue is that the game lets you do this, it allows you to use create docking (no warning) and it allows you to create a docked entity while old docks are in use. The system doesn't work well with both dock types on the same entity.
The result is that the newly created entity is docked, but completely misaligned. Probably more issues with it...
Use that ship to try it out.
-Confirmed-
Get any ship with the old docking system, enter build mode, go to adv. and create docking. I am assuming that one should not be able to use rails while using the older system.