I guess I still don't understand. On most machines, when winding a bobbin, you thread the machine completely differently than you normally would when just sewing. I don't understand why the thread would be going through the take up lever at all when winding.
What machine do you have? What does the owner's manual or instructions say regarding winding a bobbin? I'm assuming you are winding the bobbin on the machine, not on a separate bobbin winder? Can you post pictures of what you're talking about?