(((Owlie))) I hope you are feeling better soon. Is there any chance at all that the saddle might not be entirely straight? I know with my own saddle, because of quite uneven stitching, it can be a bear to get it to line up properly because the eyes wants to use those stitched lines as a guide. I know that wouldn't explain everything but it was the first thing that sprang to my mind.

What kind of pedals do you have? One of the reasons I changed to Speedplay Frogs was the SPD pedals hurt my knees, in the inside if I remember correctly.