So far as I can tell, the flagship has been set correctly in fleet data; only one fleet member returns true for isFlagship(), and it is the same one as returned by fleet.getFlagship(). It's a manually created fleet, yeah.
I'll see later if I can generate a small sample fleet that repros the issue.
I created a custom star system, and added the hyperspace objects manually.
Now the star system name NEVER show on hyperspace, including you can't select it as gate destination when gate travelling.
How I fix that?
And no, the thing that lights out mod does is not what I want...
At a guess, the system needs to have its hyperspace anchor set to appear on the map (which would explain why Ziggurat blacksite doesn't have it).
The javadocs are contradictory and out of date, but: Try calling system.generateAnchorIfNeeded to make the system appear.
I had to go poke in the source to find it.
Basically the map shows as valid systems and gate destinations, only jump points (not gravity wells), and they must end on a star. (or nebula, I assume).
A system anchor is NOT enough. A gravity well is NOT enough either, it must be a jump point, and its target must be a star, not another jump point, not a planet, etc... must be specifically, a star.
What the code does when rendering the map is is call a function on the jump point itself (thus gravity wells don't have it), and the jump point function grabs its destination, then calls "isStar()".