I've had my box squats reviewed on this msg board, and I'll quote benchmonster:
"you have to sit BACK and not down on the box. When viewed from the side, a good squatter's knee's will never move forward out over his toes. Knees must stay in the same spot as when you are locked out. Think about sitting back to the point that your knees are actually farther back when sitting on the box, than they were while you were standing. It can be done, but only with a box squat."