Car guys often talk about "bedding" brake pads to prevent "rotor warp". Braking heats up the pads causing them to leave a layer of pad material on the rotor. If you brake hard than come to a complete stop this can leave a spot of extra thick material in one spot. The brake action is no longer smooth, causing the brakes to pulse. On a car this causes the steering wheel to shimmy, like the rotors are warped.
Try cleaning the rotors with solvent and taking some fine sandpaper to the pads. If that doesn't work remove the rotors and hit them lightly with a sander as well.