I just ran an NX2 batch job on a folder of NEFs to convert from Adobe RGB to sRGB and noticed that the PM crops shifted and/or changed size and aspect ratio. Some of them may have even been lost completely -- it is hard to tell.
I realize that you have no control over what NX2 does to the NEF files, but it is unfortunate that the PM crops can not be maintained across NX2 saves. Have you ever discussed this issue with Nik/Nikon development? Maybe in a future update, they could not trash your crop data. Maybe (in some pretend universe) they could read and honor your crop data. Alternatively, would it be possible to save your crop data the same way NX2 would as an edit step? That way, it would not only be preserved, but recognized by NX2 the next time the file was opened without NX2 needing to do anything special. My guess is that Nikon doesn't share that information. It sure would be nice if they would open up the NEF file format including how they store the edit steps so their software could play nicer with others.
Thanks,
Danny