I have two janome machines and neither one have a 1/4" seam at the default center position with the janome patchwork foot. Annoying-it's a good thing I love my machines. Like Patrice, I don't usually worry about it once I get it right for one project. I sometimes have several projects going at once and don't want to worry about changing my needle position every time I sit down with a different sewing job. Plus on my first quilt top with my new machine I had it perfect, then it wasn't, then I redid it, then it wasn't again, and I finally redid it one last time and vowed I would not even bother to check it. It all fit together fine, even my piano key border.
Also, I look for patterns where it doesn't matter.