In the last update, spawn on squad leader is forced to 'disabled' for ctf. The side-effect, that we could not test without the mod being white-listed, is that the game allows that for classic only. In other words:
CTF + Realism, Action or Custom = Server Unranked
A temporary solution is to play Classic. The issues has been reported to TWI, and they will allow spawn on squad leader to be disabled with Custom too, in the next game patch. In the future, we won't assign the same variable, so the global server setting won't be affected.
If your server goes unranked after playing a CTF map, open your WebAdmin and set Gameplay/Clan Match/"Spawn on Squad Leader" to Enabled, Save, and make a map change (or restart the server).
Note: This has no impact on CGT_CD.