Originally Posted by
BSLeVan
Keep in mind that a really stiff sole (e.g., carbon soles) would negate any need for the soles to be flat on the pedals. With a stiff sole your foot won't know if the bottom of the shoe is flat on the pedal or not.
This sound like you don't have enough float in your pedals (Speedplays would cure this as would other pedals with lots of float i.e., more than 12 degrees), or that your seat could be just a tad higher. Either too little float or lack of leg extension on the down stroke can cause knee problems. The cheapest way to experiment with this is by raising your seatpost 1 or 2 cm (this is a very small amount) and seeing what happen over the course of a few rides. You can always lower it if it turns out not to be the problem.
I think the part about float would be the problem, or part of it. I still would like to have more contact with the pedal though.
I just lowered the saddle because I was extending my leg to much and that was giving me knee pain as well. The saddle is about an inch or just less than that from having my leg completely extended.