I don't know if this will help everyone (or anyone). But I had the "Shipyard won't save my new ship problem". I uninstalled GalCiv2 through SDC and then deleted all the folders associated with it. This includes the folders under My Games in the My Documents folder. Then I restarted my computer. Then I reinstalled ALL of the files.
My next problem was that when I went into the game, I had no text on the buttons in the opening screen. I was a bit annoyed at that point.
So I turned off my computer for the night. But of course, I couldn't leave it alone. So I fired the comp up. And I hit the new (remember what I said) shortcut icon that pointed to my GalCiv2 Launch file.
Suddenly there is the text. So I started a game with advanced tech so that I could design a new ship. Designed and saved it with no problem. So I saved a game, turned off my computer, rebooted and hit the icon again. And there was my new ship. No probs.
Just thought I'd pass my experience on. Incae it helps anyone.
Now I must go pass out.
I hope it wasn't just a dream.