What I would do, to eliminate this, just re-bed the pads to the rotors. Find a place where you can do a few threshold braking exercises 5 or a little more 80mph-5mph cycles (do not stop the car completely) then drive around without touching the brakes or engaging the ebrake. If it gets better after this it might be brakes related if not you go to the next idea.
As described in the stoptech link posted earlier in the thread, it's unlikely that it's warped rotors; however, it could be pad deposits baked on to the rotor. You get those if you make a hard stop and leave your foot on the brake, clamping the pads to the hot rotor. The way to easily avoid this is to scrub most of your speed in advance of where you need to stop, let off the brake a moment, and then finish coming to a stop. That gives the rotor a moment to cool from its peak temperature, making it less likely that you'll bake a layer of the pads to it.