Hello again, blisterful! It just dawned on me exactly what you are referring to on threading the needle! You don't mean just putting the thread through the needle itself, you are talking about threading the entire upper thread from the spool to the needle! And yes, you do need to have the presser foot up when pulling the thread through the thread tension area! If you pull the upper thread through this area with the foot down, you have the the upper thread tension engaged and yes it will mess up the timing on your machine every time! So sorry I did not understand this when I first answered you! Patty