Jpegs are processed in the camera using the camera settings.
NEFs are the RAW sensor data without the camera settings being applied to the recorded image. Only Nikon software, Nikon View NX2 or Nikon Capture NX2 will apply the in camera settings for when the image was shot. The Nikon products can also have over ride settings that could change the displayed image. 3rd party products like the Adobe products will not apply the setting as recorded by the camera but will apply a preset set of image processing settings.
With a sample image and EXIF data it is very hard to determine what is happening.
Many users with the higher mega pixel cameras and advanced dSLRs have problems hand holding the camera still or properly using VR lenses.
There could also be issues with an uncalibrated monitor or printer so the colors do appear correctly.