I find on my Bernina that even when I sew so that I can just see the line on the plate in front of the quarter inch foot, I still have a tendency for being on the small side. I move the needle just one place to the right, even in the space of the quarter inch foot and single hole throat plate, and it is much improved.
I think just that tiny movement makes up for the fabric/thread thickness Rosemary is talking about.
I was going to ask the technician to look at the needle alignment when the machine goes in for its service but I'm so used to it now I can compensate.