One other thing to consider is your training volume. I used to use a workout program that had me squating 2x per week with one session higher weight and the other lower. The lower weight workout was still too heavy, and the overall stress on my knees was just too much. After about 3 weeks of this my knees hurt pretty bad.
On the other hand I did madcow's 5x5 dual factor and was squating 3 times per week with no knee pain at all. In fact, my knees feel stronger than ever and I am squating with 505 lbs. This routine worked because one of the 3 squat workouts is low intensity and the other is just one all out set. Take a look at the volume and intensity of the sets that would effect your knees and adjust it down.