This may have something to do with the issue:
When I look in the Research Center, it says that I have not yet researched "Battle Cruiser Doctrine" (first screen snapshot below).
However, as shown in the second screen snapshot below, I have built Cruiser class ships. It is hard to see them behind the sun, but that is a subject of a different post.
Not having researched "Battle Cruiser Doctrine" yet would explain why I cannot see my custom cruiser ship, but it does not explain why I can build a core Cruiser class ship.

