I agree with Jim: back focus is what you've got, and the fact that your focus patch won't align at infinity is indicative of an out-of-adjustment rangefinder.
Have you tested the near focus of other lenses that you own that also have a shallow depth of field, to see if they too back focus? I find focusing on a few lines of text to be a good test, as it's very easy to pinpoint the plane of focus.
As Jim says, you'll probably find that once infinity focus is calibrated, the near focus problem (assuming it's the camera (likely) and not the Nokton) will sort itself out.
Any camera technician familiar with rangefinders should be able to adjust the R-D1 quickly and cheaply, as it's a straighforward job. It's also easy to do yourself.
To do it yourself, you need some wooden cocktail sticks, decent screwdrivers (00 crosshead, 000 flat) and good lighting so you can peer into the camera's innards.
First, you need to remove the hot shoe (see
http://www.rangefinderforum.com/forums/showthread.php?t=18901). You'll then see three screws (a clearer view is here:
http://www.rangefinderforum.com/forums/showthread.php?t=31755) - the large screw directly below the cut-out in the top plate is the third of three screws under the hot shoe (counting with the back of the camera towards you): if your viewfinder patches coincide vertically, you don't need to touch this screw. Instead, what you want is the middle one (screw 2), which adjusts the horizontal alignment: turn the screw clockwise to move the finder patch to the left. It only needs to be turned a few degrees.
Once your viewfinder is aligned at infinity, check the near focus (leave the hot shoe off). Hopefully, it's now spot on. If not, close focus will only be a little bit off, and you can adjust this with the first screw under the hot shoe. This screw actually adjusts the sharpness of the focus patch in the viewfinder but as a side-effect it also affects the horizontal alignment slightly (but much less than screw 2). Turn this screw a few degrees clockwise if the camera is still back focusing, until the close focus is spot on (this small adjustment won't have any impact on the patch sharpness). Now, recheck infinity focus, as you may need to make a minor adjustment to screw 2, and recheck the close focus. Hopefully, both close and infinity focus are now both spot on. If either is still a little out, adjust screws 1 or 2 again as needed - you shouldn't need to do igo back and forth between the screws more times than this.
