Unfortunately, the answer is: It depends.
Flag behavior and HUD appearance can be extremely unpredictable if you don't take a few precautions. If the flag -home- position is dynamic/changing, you may have to add a second set of non-template'd flags into the map and disable (not kill!) them before you spawn the templates of the "real" flags to get consistent map startup behavior. The order is important. Likewise if the capture points are dynamic/changing, similar steps need to be taken.
A logic_auto with delays to enforce order of actions has proven invaluable, for me.
If the flag/HUD behavior and appearance is inconsistent AFTER the map has spawned and play has been ongoing for a few minutes, then the problem may just be in the flag specific events and how you're handling them.
In my maps, I have never seen the HUD update properly for a flag carrier unless the flag is removed by a player death, flag capture, flag drop, or roundactivate event. I've never used an extremely large capture area either, so there may be unforeseen buggy behavior in dynamically disabling and enabling that with players already in it.