When you use it, do you keep your feet parallel? Since the foot pedals are so big it's easy not to. I know my feet tend to migrate to not quite parallel and I have to pay attention to it and re-adjust. I get it in my knees if I get lazy with form on a spin bike too (since it doesn't fit me as well as my bike).
Uugh.. Everything hurts when I use the elliptical. My feet go numb, my knees hurt, my ankes feel weird...I hate those things. Apparently I need to work on form too. :,)