My guess it's your seat and/or bike set up. Make sure you "fit" your bike. I see a lot of people ride too high or too low (eating their knees)...A bike shop should be able to set you up properly. Basically, only a small bend in your knees when fully extended. If you extend too much you're "rocking" on the seat.

Go for "regular" or "smaller" looking seat. The seats with the gel, or that are really wide are great for 5-10 miles, but after that, they hurt more than they help. (and truthfully sometimes you have to try several seats to find "the one"...)..A good bike shop should be able to let you try out a seat for a few days, or order a seat on line (bike nashbar or performance bikes) and then you can return it if y ou don't like it)