It is no longer recommended to use the standalone Nikon Transfer program. Use Transfer that is part of ViewNX 2. Nikon says the standalone Transfer software is "for older computers only." (You will have to click on "Nikon Transfer" or scroll down to the Nikon Transfer section to see it.)
In Nikon's description of ViewNX 2, they state (last bullet), "Please note that the transfer function will not transfer images from serial connected cameras. Use of a memory card reader is recommended." You did not mention how you were transferring, but I thought I'd mention it.
You may know all of this but I was not clear on how you were actually trying to transfer your images.