Sounds more like you are developing patella femoral disease to me if all that hurts are your knees. This is common when doing heavy squats. Quite a few of our patients have this same problem. Just drop some weight off your lifts, and be sure to wrap your knees. I had to drastically back off the ammount of weight I am using on all lifts due to the ammount of strength gains on my current cycle. The last thing you want to do is rupture a tendon due to doing to much too fast.