Tried your method Thecw, but got no job. However, when I was messing with it I added a piece of equipment and the new save of the ship started to show up in the shipyard list and also in the design folder. I have no idea why it did this.
The adding of something marks the design as 'modified'. The designer only make a real save (to file in the Designs directory) if he think there has been a change. That is why step 8 in my procedure is essential. if not done the designer thinks there is nothing to save and consequently does not even try.
I can imagine several things (bugs) that could cause the 'not-saving' behaviour: The 'modified'-flag is not properly set (during design alteration) or read (when you close the designer), the target design file might be in use (by another thread or antivirus[?]).
I wonder if it had anything to do with that I cheated my way to the large hulls confused the game.
When i am going to design a ship i quite frequently start up GalCiv3, create a new game, unlock all the techs, and then do my thing. So i too 'cheat' my way to the larger hulls, and i have never had any problems because of that, nor have i heard of anyone having the unlocking of techs cause the 'not-saving' problem. In my regular games i never (unlock) cheat, because that messes up everything, so if i design a ship while 'in-game' it is one with the hull size and techs available a that moment.