You are geotagging NEF files, right?
Photo Mechanic doesn't try to modify the Exif information in a RAW file such as NEF. So it adds XMP information for the GPS data, and unfortunately Nikon's software doesn't recognize GPS in XMP. Of course Nikon's software can modify the Exif in a NEF file since they own the format and know all about its internals. Photo Mechanic looks first for the Exif GPS data, then falls back to XMP on reading. For writing GPS, only JPEGs currently have the Exif data modified for adding GPS data.
--dennis