Hm, so today I was playing as Altarians, and decided to try my hand at designing ships. Rather than use a core design, I jumped in and made my own colony ship. It wasn't all complex or anything, just the big cargo hull and a few pieces of "jewelry". I decided not to add any modules yet, I just wanted a shape. So I saved it as "Colony Transport" and gave it a description, and I was happy with it. I saved it as a Template only.

Later I decided to Upgrade it (there's no option to "Use" a user-made template, for whatever reason). I added two of the mk. III engines (I forget which), resulting in a speed of 6. Added the best sensors available (mk. IV?), also giving a range of 6, then added two life-supports. Then I saved the changes.

Suddenly all the modules I added vanished, and it looked the way it did before I added anything! Except that its stats staid the same--6 speed, 6 sensor range, etc. It was so stupid, I did all that work to have a ship that shouldn't be doing anything but floating through space... and the modules were invisible!? Bah... well I used it anyway cuz I didn't feel like making one from scratch. No idea why this happened...