I just started toying around the idea of creating my own ships last night. So I spent ten minutes doing it, saved the design, checked to make sure the design was still there when I went to the builder (it was), then quit the game. Next time I loaded my game, the ship wasn't available. The ship's data files were created and are located in the appropriate place in my WinXP user profile.
So I went and designed a brand new ship in the builder, but this time actually saved my game prior to exiting. And this time when I restarted the game and loaded the brand new save game, the ship was available.
I don't have to actually build the ship in my starport. I simply have to make sure I've saved the game I used to design the ship to ensure it's available in the future.
So note to everyone - make sure you save your game, not just your ship, after designing new ships.
-HM