Are you by any chance using Nikon Transfer to copy the files from your memory card to your computer? If so, that could be the problem because there is a known issue with Nikon Transfer making some small change to each file. If this isn't the problem, are you using LR to import directly from the camera or from the card via a card reader? That could be the issue. Try copying the files using Windows Explorer or Mac Finder to a folder on your hard drive and then see if LR can import from there. That may help you narrow down the issue. I have a D300s and have not had this problem with LR 4.4.
John