I've never had this problem before. I put 635 photos in a folder, a combination of jpg and NEF files. I chose Synchronize but only 81 imported. They were all jpg. Why doesn't it import the other jpg's and the NEFs? I restarted and relaunched but still won't import.
One reason is that the NEF files have already been imported into Lightroom, and so there is no need to import them again.
Another reason is that your camera is not supported by your version of Lightroom. What camera, and what version of Lightroom are you using?
Yet another reason is that if you used certain versions of Nikon software to move the photos to your hard disk, then the photo header might get corrupted and then you would have to use some free tools to uncorrupt the headers of these files; or use Lightroom to obtain the photos directly from the camera card.