I believe the maximum number of players that may be in the game is hardcoded to 35 (in FfH, it is lower in normal BtS) in the DLL, so the computer cannot add another slot beyond that in mid game. Kael had changed it to 40 (I think) shortly after BtS made it possible for modders to change this, but he reduced it since (at the time, before introducing Minor leaders) having more than 35 players would require duplicate leaders be in the game at the same time. I'd recommend increasing the limit again.
I just remembered one time several version back when I liberated a colony after killing off a civ, and the new civ/leader took the slot and name of the old. That Cardith Lorda looked a lot like Arcturus Thorne.