This has been present since shipyards were introduced. It was mentioned in task T551 but is still present in the current release.
In short; the shipyard will spawn a ship based on a blue print or design properly. BUT when you unload the sector, everything except the center section of the ship will be missing, Meaning only the "shipname".0.0.0.smd2 is properly saved to the data base and nothing else.
I would have included logs, but the logs do not show any kind of saving error that I could find. I am including the ship files and how to reproduce the bug.
So What I did was save a ship to blue print. name: LongShip I then loaded it into a shipyard via blue print and had the shipyard make it. It spawned from the shipyard correctly. I then exited the game, unloading the sector. When I logged back in the front section of the ship was gone.
I saved the bugged ship as "longshipBUGGED" now in this saved file the front section of the ship Longshipbugged.0.0.1.smd2 is there, and has the correct file size, but if you spawn the blue print the front section is missing.
To double check this I created a 3rd blueprint "LongshipDELETED" from the clean working blueprint "longship" and manually deleted the front section of the ship, just to make sure. It turns out looking the same as the "longshipBUGGED" blueprint.
I dug deeper and looked through the server database files. The front sections that are visibly missing are in the server database, and they are the same size as the unbugged version of the ship.
So I would have to assume this is some kind of database saving/loading error. AND yes the shipyard is more then long enough to spawn the ship :)
I have included pictures and blueprints of the ships I used to test this.
Go get um boys! Thanks for all your hard work =D
EDITED: I misread some of the file names in the database and thought the bugged ships files were smaller, but they were not. Now this happens with just about every ship I put into the shipyard that has more then one section. But when I built a ship in the shipyard that had multiple sections it turned out fine with no saving errors.