Okay, so I was playing about with a new character, and I managed to keep my old ship from before it gets repaired by the shipmaster (which has slightly darker colours), and still receive a free new one. What you need is another ship from another character in the vault. When you make your new character and finish the first mission, the ship you get is different to the repaired ship, slightly in terms of colour, so, when you go to the tower for the first time, you get out the ship that's in the vault, make that your active ship and put the original ship in the vault, then you go through the mini missions but when you get to the shipmaster it shouldn't come up with anything when you go to her. I went to orbit and back to the tower, and it gives you the gunsmith mission then back to the shipmaster, only this time she gives you a new ship while the old one stays in the vault, so you now have the fixed up ship, and the old one you started with. I know it's not groundbreaking or anything, but I thought it was pretty cool Edit: I've just compared the two in orbit, and I would definitely say there is a comparable difference between the two, colour wise