I am playing the latest beta. I go into the ship creator create a ship just fine. In fact I absolutely love the new interface its basically a dream come true. Well anyway like I always do I just create an empty hull an save it. When I want to create a specialized ships I then go back in and upgrade that ship, put on the properly applicable modules, and then rename it to reflect the mission that it was designed to fullfill. The actual problem then becomes that I save it under another save when I am done so that I still have the empty hull to work with, and what actually occurs is that the original hull the I created disappears and only the newly upgraded ship is there.
This has actually happened twice to me so far, since I've only created two ships. And once the game actually crashed because of this.