When you start looking at 100% on an 18 megapixel, perfectly flat sensor, flaws that used to be elusive start to become easily visible. It is the tradeoff for high resolution digital. On film, most users would not notice most of these slight misalignments of body or lens unless they routinely printed 20x24 or larger...and only then if their enlarger was perfectly aligned, they were using a glass negative carrier and a good enlarging lens. Most people never got even close to that... many photographers never printed over 8x10. Now testing a lens to its breaking point requires no skill at all -- just open up the file and click on the magnifier. So in a way, it is not that the old Leica lenses did not have focus shift or were built so much better before, it's just that the tolerances have to be so much more critical these days. And of course, anything could be responsible for getting a lens out of alignment, and it is not always that it left the factory that way! It could have been knocked around during shipping, or it could just be that your particular body is on one end of the tolerances and your lens on the other, and that particular combo is out enough to make a visible difference.
The best solution is to send your body(bodies) and lens (lenses) to someone like DAG or to Leica to have them matched. And then keep your eye on things to make sure they don't change.