Hi Sam,
If all of the grades for this assignment have shifted, I wonder if the scale in use for the assignment has been changed (after the grades were assigned)? I just ran a quick test where I set up a scale matching yours, set up an assignment using that scale, assigned some grades, then changed to another scale (P/M/D/R instead of R/P/M/D) and the grades all changed to the one in the same position in the new list as the grade I assigned in the initial list (i.e. R became P, P became M, etc - as per your scenario). If this is the case, changing the assignment back to the original scale should correct the grades (though of course any grades assigned after the switch would then be wrong).
My first thought was actually that the scale itself had been edited, but you can't edit scales which are in use - so I moved on to the idea of changing the scale assigned to the assignment.
HTH,
Paul