When I was in vision training a few weeks ago, I was informed that the witness marks are pre-molded into the robot prior to assembly. They're good for getting a rough calibration, but unfortunately they're often off by over a degree in rotation.
I'd recommend calling your FANUC rep and requesting they perform a vision mastering. They'll attach a camera to the robot and it will remaster itself using a calibration grid.
We did this in class and found the witness marks were about 0.5mm off.
Note - vision mastering only masters J2~J5. J1 and J6 aren't re-mastered (though, they're not critical anyway to generating straight lines)