I did see the following on wikipedia, http://en.wikipedia.org/wiki/Disc_brake
I did use the Posi Quiet pads that came with the rotors.
"This type of thickness variation has many causes, but there are three primary mechanisms which contribute the most to the propagation of disk thickness variations connected to uneven pad transfer. The first is improper selection of brake pads for a given application. Pads which are effective at low temperatures, such as when braking for the first time in cold weather, often are made of materials which decompose unevenly at higher temperatures. This uneven decomposition results in uneven deposition of material onto the brake rotor. Another cause of uneven material transfer is improper break in of a pad/rotor combination. For proper break in, the rotor surface should be refreshed (either by machining the contact surface or by replacing the rotor as a whole) every time the pads are changed on a vehicle. Once this is done, the brakes are heavily applied multiple times in succession. This creates a smooth, even interface between the pad and the rotor. When this is not done properly the brake pads will see an uneven distribution of stress and heat, resulting in an uneven, seemingly random, deposition of pad material. The third primary mechanism of uneven pad material transfer is known as "pad imprinting." This occurs when the brake pads are heated to the point that the material begins to break-down and transfer to the rotor. In a properly broken in brake system (with properly selected pads), this transfer is natural and actually is a major contributor to the braking force generated by the brake pads. However, if the vehicle comes to a stop and the driver continues to apply the brakes, the pads will deposit a layer of material in the shape of the brake pad. This small thickness variation can begin the cycle of uneven pad transfer"