Nikon Transfer, as mentioned in the OP's original message, is obsolete software and WILL corrupt NEFs as far as being read by Adobe software. It is likely the OP is using the Nikon software from the previous camera model to view images from a newer camera.
The best course of action is to recopy the images from the card using a file-system utility like Explorer or Finder and never touch them with Nikon software.
The utility at queensu linked above will fix the images but only works for some cameras.
