Besides that stuff, I think the #1 spark must happen at the same time in the cycle for it to run properly, so clamping to #1 you should still expect to see the mark on the crank pulley. Unless the pulley is separated and spun, but that should be obvious..

Make sure the light is set to 0 and the procedure should be by the book. You could adjust the offset and see if that brings the marking around, if anything it could give a degree number to think about.