Pad material needs to be bedded into the rotor. Pulsing is most often due to uneven deposits caused by improper bedding or hot pads/rotors being left in contact.
In some cases, you can remove build up by rebedding the pads. Sometimes a more aggressive pad is needed to remove the old material first.
For more information than you can stand, check out the tech pages at
www.Stoptech.com
Directional vented rotors typically outcool non-directional.