Yes, that is the cap limit. The default is 3 caps wins a round. The server console command is 'tf_flag_caps_per_round' and is 3 by default.
I am at work at the moment, but you may be able to set up an output on the flag that causes the capping team to automatically win the game to override this. Have a look at the 'OnCapture' output for the item_teamflag, and the SetTeam and RoundWin inputs on the game_round_win entity.
Not sure if it will work, but its worth looking into.