POSSIBLE SPOILERS Possible difference between the the final five and the other cylon.

[TPL2005]

If the part of the script for Razor i read is for real:

Spoiler:

Adama found a cylon lab just before the end of the original war, where humans were being experimented on such as having electronic implants put into them. Perhaps the final five were originally human but had cylon implants and techonology put into them.

But why the other cylons can't remember them or at least talk about them i can't explain.

[Sauron18]

Spoiler:

Actually, RDM & Co. have confirmed that the Final Five are full Cylons, and that means they were created by the Cylons, and weren't based on anyone.

What their "fundamental" difference is, we don't know, but what you read is most commonly assumed to be the Cylons reverse-engineering human bodies in preparation for making their own.

They are full Cylons, so their fundamental difference is probably going to be something that doesn't actually deal with their individual bodies, but rather with something else. This could either be as simple as their allegiance, or possibly as complicated as them being the only copies of each model.