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I may have just found my own answer. Please let me know if this is plausible. I only notice the problem some of the time, and looking at the files I see when it does happen I have the Active D-Lighting set to extra high on the camera. Nikon software reads this fine but can Adobe somehow not adjust for that setting? I honestly think that is the issue. I will test in daylight again tomorrow to verify. Thanks!
I think the ViewNX software re-writing the metadata for the raw images that's why its unreadable by Lightroom.
Please try and import images directly in Lightroom from the SD Card and check if that works.
Also, you can refer the below link to fix the existing images.
Yes, Active D-Lighting is the problem.
When ADL is set to "low", all the processing is done in the camera, thus causing no problems with third-party software.
At any of the higher settings, half of the ADL processing is in-camera with the second half done in the Nikon software for post processing. Since no third-party software reads the ADL data -- nor knows what to do with it -- it results in underexposed images when not processed with Nikon's software.