I keep thinking that the final answer has to do with the resurrection ship. The oddball theory I have was that the Cylons were trying to improve their abilities, and decided to make a method of saving and restoring their best fighters/pilots/ships, and built the resurrection ship, but then the final five popped out of (to them) nowhere. So, confused, they put them among the humans and then started trying to replicate the idea as ‘skin jobs’, and created the seven. And while they could copy those seven, they couldn't figure out a way to make any duplicates of the (first) final five, so in many ways they're somewhat mystical to the cylons, especially since they don't understand or know who/what/how those five were created.
How they were transmitted from Earth to the resurrection ship was unknown, but suspected that they were all very strong willed cyborgs, their data flung out by the nuclear explosions, which took a good long time to reach the cylons, accounting for the time difficulty.
Eh, not sure I buy that...