The alignment is off because you didnt drill the second hole from the same reference side, you flipped the board over to drill the second hole so you used a different side as reference point. If the jig center is of by 0.5mm from 9mm center (because it’s not a super accurate tool) because you drilled from the opposite reference side it can create a 1 mm difference. I believe that’s why you dont have a perfect alignment. If you drill from the same reference point the alignment should be better! But thank you so much for taking your time to show and explain the jig! Great work!