I don't know if this has been said, but I sure couldn't find anything on it in the patch notes.
Maybe it's a bug, but it seems to me that if the enemy has your flag for a certain amount of time, it becomes visible on the map. So far this had happened about 5 times as far as I can tell.
Is this just a bug or have Blizzard implemented it as a way to curb 45 minute matches? Any guesses?