As far as I know, there is a hard coded limit of 31 civs plus 1 barbarians in the game, and you can't make any more than that. If you replace a civ with a custom one you shouldn't have any problems, but I don't know about adding extra civs. If you direct your question to the modding forums, I bet someone there would be able to give you a better explanation of what's going on.
Another thing I thought of is that maybe if you are changing the default scenario file, it automatically reverts to its original settings, unless you save it as a seperate scenario. When you add the civ, click on "Save As..." so that you can choose a name and location for it. If you then open the save and the civ still appears to have disappeared, then I'm out of ideas.