Terry,

Things I would suspect as being trouble points are the +.001 on
the shoulder of the backing plate. If it's a "very tight press
fit" as you say, you may be introducing enough stress into the
chuck body to warp it slightly. Can you skin off another half
a thou? As Grant said, undercutting that shoulder is important
too, for the reasons he mentioned. Are all of your mounting
bolts torqued down approximately the same amount? If the chuck
body is larger in diameter than the backing plate you could
mount the chuck on the lathe and indicate the back of the chuck
body itself to see if it is seated squarely on the backing plate.
One way or the other you ought to be able to track down the error
and resolve it. As others have said, scroll chucks are not the
most accurate work holding devices, but their inaccuracy has
to do with the scroll and the jaws, not necessarily the chuck
body. If I were you I'd try undercutting that shoulder first
and go from there.