My uneducated guess for the discomfort could be a combination of things. First, I need better footwear. The two years I trained without discomfort, I wore cross trainers. The cross trainers have worn down from wearing them and my stance feels unbalanced. Correct me if I am wrong, but from my understanding weightlifting shoes are more appropriate for Olympic squats than cross trainers.
Second, I have always trained at home. I moved into a new first floor apartment recently and the entire floor of the apartment tilts downwards towards the street. I tried squatting in both directions, however my stance felt unbalanced either way so I started squatting with a 1/2 to 5/8 inch board underneath the heels of my feet to even things out. The board worked as far as solving the balance issue, however I started feeling discomfort in my knees after I started squatting with the heels of my feet underneath a board.