(my apologies to the non techies, just skip this annoying post)
Even you marked the topic as SOLVED (and a moderator could close it), i tried to understand what is happing in you workflow to find out if there is a bug with general raw/or just with Nef.
Breaking up you Batch; the first two steps are difficult to examine as no output is possible. I assuming Photo Supreme load the nef (libdcraw) in memory resizes and sharpen.
The third step is the first producing an jpg output file. In your original batch with 'Write metadata; if available" enabled, it is going wrong: The beautiful lady on the jpg thumb is rotated wrong by adding a 90°to the already 90° turn of the original, resulting in a horizontal position (180° turned compared to the original). The nef is still alright.
In windows and FPV both files are correctly rotated! The jpg orientation i set to 'Normal' even the image is rotated correctly.
It is getting more weird when i open the jpg in PSe. In the PSe properties of the file, i find:
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While the idimager section looks like a recipe and i doubt PSe will apply this recipe to the image, the first part is indicating the tiff orientation to 1, and this is not 'normal'. However the image is 180° turned compared to the thumb.
I retried the third step but now with the "Store created file as new version" disabled. This is resulting in the same wrong jpg. However, also the nef is turned 180° IN the other direction;
I'm starting to loose any confidence to solve the problem and are in urgent need of a cup coffee, but not before i fired exiftool(GUI) to get at least my orientation back:
Exiftool indicate :
Exif (IFD0) - Orientation : Horizontal (normal)
XMP (XMP-tiff) -Orientation :Rotate 270 CW