I'm betting that the colonists turn out to be the 'Cylons' of a previous generation, and the 'This has happened before and it will happen again' quote is quite literally true. Every x-thousand years, 'humans' invent Cylons, they rebel, they become organic, and the last remaining 'humans' end up making nice w/ the Cylons and interbreeding w/ them to unlock the genetic key. Time passes, everyone forgets their origin (maybe they go out and colonize, why not) and then the cycle repeats.