I had a similar problem to yours using Nikon Transfer, but I only noticed it when using Helicon Focus software (for focus stacking) which refused to work with the images from my (then, in May 2012) new D800. Previously with my D90 all was OK.
The folks at Helicon agreed that there was an issue with the image files but couldn't identify what was causing the problem.
Luckily I had just acquired a Kingston card reader to alleviate my frustration while waiting for the D800 to download a truckload of data and, voila, the problem with Helicon disappeared as soon as I started using the reader.
I reported the issue to Nikon UK but I've never tried newer versions of Transfer to see if it was fixed.