the look pedals and platforms can also be adjusted (forward or back) and your seat can be adjusted backwards or forwards to simulate different leg distances. i am just illustrating that it can be one of several things, but the responses you have gotten about saddle height are GENERALLY correct and very good.
when you adjust anything on your bike do it in little tiny increments. a mm to a cm here or there can make a big difference. the more i talk to people the more i hear about people tweeking their set-up little by little to get that perfect set-up.
remember: biking should not hurt (your joints, etc)- don't let it go. when i started out i had the same problems and didn't have this forum to bounce things off of people and suffered for many months.