all capships have custom names and they can be renamed. SO you could rename your 1st ship to "Flagship".

I make diffrent fleets all the time so i havent seen that problem before.

And a litte tip, when you play as TEC train your caps to lvl 4 before you throw them in combat

Finally someone mentions this again! I brought up this annoyance and know exactly what you are talking about Kodiak. I don't know if you can fix this by doodling in the scripts but its worth a try. I'm in NJ now so I can't help you look for a script but you should try finding one that refers to Flagships and my guess is that it would be in the gameplay constants script. There might be a chance that you can fix it in there. As I said, I kept bringing this up (in things like "what do you want in the next patch" and I always said "Fix the flagships!") Of course nobody listened to me and though it isn't really important, I always like knowing I have a flagship! I also think they should put a designate flagship button as an option and give flagships some sort of combat bonus or something extra.

(Sorry if this was sort of rant-ish)