Not being able to get your knee over the pedal may be a blessing. Be absolutely sure that you are doing the measurement correctly with the bike sitting on a level surface. If the bike is not level, then the plumb bob can't produce a proper reading. Some experts go from the very front of the knee to the front of the crankarm, which is easier to do. Here are some articles debunking KOP.

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