Assuming your hardware is not defective and the pedal adjustments are correct...
1)
A pinched hard line someplace. But then that would seem to show itself in the bias front to rear. That is, if the pinch were in the front, your rears would lock up before the front reached adequate pressure for full stop power. You might not even notice a pinch in the rear of the system.
Proportioning valve trouble? Can you remove that from the system and go for a test drive?
Some sort of delayed boost/assist action, faulty booster?
Need to bed the pads into the rotor and season the rotors. The rotor is too slick for the pad to grab properly and so it needs to be seasoned and the pads need to be bedded:
http://baer.com/site_images/Rotor%20...%20Bedding.pdf
Hth,
-klb