Some input from my end. How is your seat height and position fore/aft over the BB between the two bikes. If you used the exact static measurements between the two, since the FS rear sags it will not be exact that same as the hardtail once you sit on the FS. You may have found the sweat spot on your FS, but those exact measurement to the hard tail may not translate to ideal. Of course the shorter cranks would make things easier, but I would probably really look at bike fit first. Also what type of pain are you experiencing in your knees, front, side, back? I see you are on flat pedals, do you use flats on the FS also. Also are the cranks between the two bikes the same spindle width. One problem I have run into if switch between bikes with different spindle length or pedals and just go by look on the pedal to place my feet, the width my feet are apart will not be the same. If my feet are further apart then ideal I will get knee pain. Therefore on the bike with wider spindle/pedal interface I have to be conscious that I put by feet more inward on the pedals.