Chereo! I have exactly the same problem of Montijin, I have tried adding a custom civilization, I've added the start position and it still doesn't appear on the list of the custom map, even though it appears on the normal game to select the civilization.
The civilization is this one: http://forums.civfanatics.com/downloads.php?do=file&id=20139
And this an image of the civilization tag on CivilizationsStartPos.xml
Thanks
The civilization is this one: http://forums.civfanatics.com/downloads.php?do=file&id=20139
And this an image of the civilization tag on CivilizationsStartPos.xml

Thanks