This may sound odd but what rotors are you using?
The reason I ask is I was told (some time ago) that IF your lbs is bleeding them using the supplied Shimano 'bleed block' in the caliper they are setting them up on the assumption that you're using ice-tech rotors which are thicker than the standard ones. Whilst it's only .5mm or so it can make a difference once the pads & wheel are fitted, especially if the caliper is not absolutely centred over the rotor. The longer the brake hose the more exaggerated the impact (more fluid to compress per mm of movement) so the rear is usually where it's noticed.
I use 2 sets of wheels with the same XTR brakes & there is a noticeable difference between them - the only difference on the wheels being the rotors.