@alisha-- That's right, it's about breed. You can't breed two Kiko goats that are not registered with an association, in fact you'll have problems registering the herd if they're not from the same association. Of course, associations want to make sure that they're not mixing DNAs with other breeds. The other bit is purely political, so to speak.
There is actually only one American association for Kikos, it's called the "American Kiko Goat Association." The other association is an international one: "International Kiko Goat Association." And then there is an American registry called "National Kiko Registration."
You can register your goats with any one, just make sure that you can breed with goats from the same association. I've been raising goats for milk for a long time now. I started raising Kiko goats about three years ago. Mine are all registered with the National Kiko Registration.