The valves on #1 should not be moving when you're setting injection. 1 must be on compression stroke so valves must be closed. #1 tdc on compression will have valves on #6 on valve overlap.
I'm not sure why it would have changed. That's not normal. What I described is exactly the timing check procedure. Don't worry about the camshaft or valve timing. As long as you are 100% sure it's #1 compression. Do what I described will be your injection timing plunger lift. In its current state. Is there a key way in your pump shaft?