There is a bug, related to things like distance between civs and requiring good starting spots that can cause not all civs to spawn on crowded maps, that might be the problem. In that case I think you're better off asking a modder like Seven05 or Gedemon if they can make a mod where civs can spawn much closer to one another than they normally would and/or don't require as good starting spots. For Seven05 I know for certain that he's fiddled with the relevant code.