No, 31 Civs (plus Barbs) is a hardcoded limit in Conquests (and in Vanilla Civ3 it was only 16). AFAIK, to date, hacking the .exe to increase this has never proven possible.
But it is possible that you might be mis-remembering? As I understand it, CivIV includes several versions of the same Civ, but run by different leaders (I have IV as well as III, but have only ever started a couple of games), e.g. the Britons(?) might be led by Boudica, or Victoria(?) -- and I think that both versions of any given Civ could potentially show up within a single game.