well i haven't tried this with that many battleships but i know for a fact whenever u buy a dragon battleship/cruiser it get's stuck in the docking bay :rtfm:
This of course on works on a server with FLhook installed and the proper additions, like all of the big servers i know for sure. In singleplayer you have to use ioncross character editor to move your character to a base that doesnt do this.
Best method is to use IONCROSS to move your capital ship to a planet. Or a station like Newark. Both are very good at undocking large ships (I undocked a Barge from Newark >_>)
In SP all ships launch from docking bay 1, so they can't make use of the mooring points and such.