if you re squating 3 times a week with any real weight your knees are going to be hurting. Make sure you give your joints time to rest if your haveing issues with them. Remeber, especially because of your special supplementation you run a higher risk of moving more than the little bits in your body can handle. Be smart, if something is botherting you find an alternative. ( I know, I know, no pain no gain but we all know what I am talking about.) also I am assuming that you are getting all of the nessacary fats and are taking joint supplements.