When I have had such a problem on other bikes/cars, usually it was down to the pads/rotors not being bedded in properly. When I replaced the rotors and pads on the ST11 00 at 100,000kms I had a similar issue, replaced the pads with some older sintered pads that were a bit more aggressive to run in the rotors, then used the new pads again and no problem.
I just replaced the pads and rotors in my car which had a similar issue - the pads just did not get on with the rotors all the time, so lead to a wobble in the steering at times under brakes.
Not to say that it could not be warped rotors or something else.