I believe I figured out the issue, and it appears its not Photo Mechanic…I shoot NEF+jpeg and backup images to both the CF and XQD card slots. I was pulling the CF cards out for ingest, but as it turns out, the D4 was making the XQD the primary card. The primary card gets the image protection/lock/tag, but not the secondary. So once I went into the Shooting Menu and made the CF slot the primary card, my tags carried over into Photo Mechanic. Problem solved. Thanks to Dennis and Brandon for their quick response!