Here's my pet theory.
The line "This has happened before, and will happen again" is the most critical line.
The Scrolls of Pythia have been violated; the "dying leader" has seen the 13th Colony. How can she have?
Simple; she isn't the dying leader. There was a dying leader, once, long ago. The prophecy was acted out by humans, who were destroyed by the Cylons, who carried a single child, part human, part Cylon, with enough genetic diversity to enable the "skin jobs" to stop being just clones and start being unique indiviuals, who travelled back to the twelve colonies, and forgot they were machines. Eventually, they decided that what they really needed was a race of robots to help them....
You see? The "humans" have been long, long dead, and the Cylons, being machines, are stuck in an infinite loop, acting out a prophecy that was long fulfilled.. and still carried down..
