I've uploaded samples generated by the camera that just came back from service. The serial number does not appear in the EXIF for the NEF or JPG files.
Well, sounds like Nikon did you a dis-service somehow because you are correct, the serial number doesn't show up in these files.
Are these files straight from the camera without any other software touching them (i.e. mount card in card reader, copy to computer, FTP)?
What about your other camera that you upgraded to v2.00 manually?
Maybe you can try re-installing the v2.00 firmware on this camera (if it will allow this) and see if that fixes the serial number.
I'm baffled... Perhaps it is time to ask Nikon. I'll see them on Saturday for the NPPA FSC in Fullerton and maybe they will have a clue. I'll also be able to get some sample files from other cameras to get some kind of consensus.
--dennis