Incorrect teams on rejoin

Using v1.2.9 of ArenaCTF, 3.9.6.7 of BattleArena.
If a CTF game is started and a player leaves, either by /ctf leave or by disconnecting and then rejoins, they will sometimes seemingly be on both teams. waitroomClosedWhileRunning is false and alwaysJoin is under onJoin.
They receive messages for both teams such as if the other team's flag is returned home, and receive the update messages telling who has the flag and the current scores twice. They cannot attack players on the other team, but they can be attacked by those same players. I've also heard that sometimes players can attack their teammates as well as the enemy team. My CTF config: http://pastebin.com/fAHWDXuM