Do you use cleats? Are you sure the cleat isn't keeping your foot at the unique angle that you and only you alone need at both the top and bottom of your pedal stroke?
My left and right foot have do not sit anywhere near the same angle on the pedals. On foot the heal to toe line is almost straight and parallel to the bikes centerline. The other is angled with the heel much closer. It does make a difference. Recently I had a cleat come loose and I got it with the wrong angle. While my knee felt good when extended, on the up stroke, I could feel a little twist that was becoming annoying. So I stopped and adjusted my cleat.
Did you ever say whether your saddle height is measured to the pedal at its downstroke or to the BB?