Are you still playing with the same ship style? If you change ship styles in the game setup screens the ships you designed using the other style will not show up.
As far as backward compatibility, it has long been known and accepted that old save games may not work in a newer version of the program. So it is always a good idea to update the program between games instead of during one.
And it should not be an important factor, either. We have asked for a lot of changes to the program, which the dev's have bent over backwards to give us. They have even put in their own personal time, long hours on weekends and late into the night, to make sure we have what we want in this game. Their compensation for this extra time and devotion to this program and its users should not be even more complaints about such mundane issues as backward compatibility. Often the enhanced functionality of the updates require that it not be backward compatible. And I would rather have a better program than worry about loading some old games I have already won (or lost, as the case may be).
No, their compensation should be, at the very least, our praise for making a great game even greater.