You may need to "bed in" your brakes. Below is an excerpt from the "technical papers" of that same website. For the complete method click
here.
"When a system has both new rotors and pads, there are two different objectives for bedding-in a performance brake system: heating up the brake rotors and pads in a prescribed manner, so as to transfer pad material evenly onto the rotors; and maturing the pad material, so that resins which are used to bind and form it are ‘cooked' out of the pad.
The first objective is achieved by performing a series of stops, so that the brake rotor and pad material are heated steadily to a temperature that promotes the transfer of pad material onto the brake rotor friction surface. There is one pitfall in this process, however, which must be avoided.
The rotor and, therefore, the vehicle should not be brought to a complete stop, with the brakes still applied, as this risks the non-uniform transfer of pad material onto the friction surface.
The second objective of the bedding-in process is achieved by performing another set of stops, in order to mature the pad itself. This ensures that resins which are used to bind and form the pad material are ‘cooked' out of the pad, at the point where the pad meets the rotor's friction surface.
The bed-in process is not complete until both sets of stops have been performed."
The quotation above in bold is describes what probably happened to your rotors. What I have found is that merely cleaning your rotors with brake cleaner or wheel cleaner will remove all of the embedded pad material and instantly smooth out the pulsation. Beware, your brakes will not be nearly as effective until the pad material is reapplied through braking several times.