I have that exact Janome Deb and have to say I have made many button holes w/it and have never had that happen. It would be my first guess that the button may not be laying flat in the tray causing the measuring difference. I also agree to go thru all the directions to make sure you have done all the steps correctly. If then, it still is missing on the stitches, I'd call your service people and see if it is a simple adjustment on your end or an explaination to the why. Do tell what you find out for that just in case...:)Skeat