It's possible that each jpeg and NEF pair is stacked together.
If you right click (or cmd click) on one of the images, under 'stacking' you should be able to select 'expand stack' or 'expand all stacks' and then you'll see all the photos. To remove the stacking all together, select 'unstack'.
If you want to change your preferences so that the NEF and jpegs aren't stacked at import, under 'edit -> preferences', select 'treat jpeg files next to raw files as separate photos'.
Regards,
Peter