There is an issue in the game where a Flag Ship will not show up in the Fleet Directory unless the Leader of the guild is online. The Flag Ship must set to public, however it still will not show up in the Fleet Directory unless the guild leader is online.

I have triple checked to ensure that the Flag Ship is set to Public, even stating such in the header of my tickets.

Here were the results of the tickets I submitted in regard to this issue:

From the first ticket submitted:

Make sure the Flag ship is set to public.

From the second ticket submitted:

This is working as intended and I should post in the Suggestion Forum on the off chance that a Developer might see it.

No response in the Bug Section:

http://www.swtor.com/community/showthread.php?p=9624088#post9624088

So maybe this is the place?