Having just aquired an old Bessa R (even the new ones are old now I guess) I do have the following theory, I may be wrong so please feel free to correct me.
The Bessa R shares a similar but not identical RF mechanism to the RD-1 right. The subtle difference is that the RF spot on the R moves with the frame lines for parallax correction. The RD-1 and R3A (and maybe the R2A) it does not.
I noticed this when checking the alignment near and far on the R, far away it was fine, close up it was slightly out untill I moved the position of my eye in the finder and all was very well. Now I guess that CV got fed up with complaints and decided that if they left the spot in the same place people would not move the view point (as I did) as the framelines move. So maybe its natural for us to slightly move the view point very slightly as the lines move, in theory anyway.
OK in a nutshell, try a distant object that has a very near point in the RF patch as well, try a stick in the ground, then refocus without changeing eye position. If its still a out of whack I'm out of ideas.
Thats it folkes.