Yeah, that's something I never quite understood about the show. The Skinjobs were clearly not Cylons. They were just an off-shoot of Humanity who, after thousands of years of independent existence, developed a new form of technology that let them download their consciousness.
I was under the impression that the Kobolians created cylons who eventually banded together to become the 13th tribe. I never got the sense that they were just another group of humans on Kobol.