It may be that your .opf file has a link to a file that is not present in the .epub. You could check the .opf file in Sigil.
I have been having the same problem for three days now, trying to upload a Word .doc that is simply four (exactly the same) word docs pasted end to end to publish as a "collection" of four books I already successfully uploaded using those same individual docs.
I then converted to HTML, and got the same "FATAL" error; used Callibre to convert to ePub, which works on my PC reader and side-loaded Nook, but that also returned the same error.
So, it errors whether i upload .doc, .docx, ePub or HTML, even though I had no problem whatsoever uploading and converting at two other vendors.
Again, there is absolutely NOTHING changed or different about this doc file (or its various conversions) from the doc files that it contains. the file size is only 6.3MB, well below the Nook Press limit.
I believe something is seriously wrong with the manuscript upload system, as several people I have spoken with have this exact same problem over many days but no such problem uploading their same files to other vendors.
Of course, it would be helpful if the error gave some kind of hint as to where it thinks the file might be lacking.
There is nothing wrong with my file, unless Nook has added some unknown requirement since I uploaded the four files this one contains two weeks ago.