First off, the civilization images are hard coded into the .exe (dont believe me? open it in notepad!)
This means that only the top 15-16 can be played BY THE PLAYER in any game. Not only will you have to re-order your civs so the ones you want to play as are at the top, but you also must make sure that the top 16 retain their prefixes (Ab_???, Lz_???). I.E. If you dont want to play as the americans, you can move them to the botoom of the list but all the Ab_??? files must be renamed, and the civ that replaced the americans on the top will now use the Ab_??? setup.
The bottom ones can be played against if you get the extra palette files (
http://forums.civfanatics.com/showthread.php?s=&threadid=19611 ). I was able to have 31 civs in my game as long I was playing as a civ in the top 16 using one of the default prefixes (Ab_???, etc).
The only bugs I have found with this do not affect gameplay too much. If you meet a civ that lies in the 16+ area of the civ list, the diplomacy may be alittle messed up (i.e. When in diplomatic conversations, they may say something like "#AIWHATEVER2") Also their pic will not appear correctly on the foreign advisor, but the game will not crash.
It is very hard for me to explain things, and I hope you understood all that. Ask any questions you may have and I will try to answer.
GIDustin