Originally Posted by james_swift
I noticed the same thing with my stock rear wheel. I ordered a custom single-speed wheel w/solid axle from Peter@Design Mobility, and the wheel aligned perfectly between the chainstays. So I'm guessing the issue is not with the rear triangle, but maybe with the spacing of the rear hub and/or the dish of the rim.
Well, a mis-aligned wheel can't be a good thing. Let's hope that James is right and that a simple truing will address the issue. If the rear triangle is mis-aligned, I don't know if you can do anything about it given Sheldon Brown's comments on frame spacing (and aluminum frames).
http://sheldonbrown.com/frame-spacing.html
-G