Saddle/fore aft positioning is not only about placing the knee in a particular position relative to the pedal spindle. Although dropping a plumb bob from the knee to the pedal spindle, or the front of the crankarm is a common practice, a number of well-regarded fitters do not believe in it. They follow the idea of getting the rider's weight properly balanced over the saddle. Most often, that's further back than a KOP check would suggest.

http://www.cyclefitcentre.com/pdf%20final%20docs/backyard%20positioning_julu_aug_2004.pdf
http://www.cyclefitcentre.com/pdf%20final%20docs/THINGS%20YOU%20MAY%20NOT%20HAVE%20KNOWN%20ABOUT%20BIKE%20POSITION_final.pdf
http://www.peterwhitecycles.com/fitting.htm
http://www.sheldonbrown.com/kops.html