I'm not entirely sure this is a problem. You might want to check out this squat analysis:
http://www.exrx.net/ExInfo/Squats.html Specifically, the site mentions that 'Contrary to propaganda to the contrary, prominent weight training authorities demonstrate the squat with the knees flexing forward at the same distance as the hips flex backwards. Fredrick Hatfield, Ph.D., the first man to squat over 800 lbs, recommends the knees to extend over the feet with the back more upright for quadriceps development. 'Strength Training for Young Athletes' by Steven J. Fleck, PhD and William J. Kraemer, PhD, illustrate parallel squats with the knees extending beyond the feet (knees moving forward with same magnitude as hip moving backwards).' Is this how you're doing it?
Patrick Falcon