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I tested my NEF files with FRV 1.5.3-1502 beta and they all appear correctly now.
I noticed that the files that showed up wrong all had a "Software" field in the metadata of "Nikon Transfer 6.2.7 W".  The ones that were showing up correctly had a Software field of "Ver .2.00".  I would guess that the "Nikon Transfer" software probably introduced the problem, and files transfered directly off the camera are fine.
Was this fix added to libraw?  We use libraw in our software.