If it seems NookPress is corrupting the epub file you know to be good, here is the feedback I got:
"If you uploaded your own .epub file and selected to put On Sale "The original .epub I uploaded", then the NOOK Book file that customers download will be the exact same file you uploaded without any changes made to it.
"The "Preview NOOK Book" link displays the contents of the Manuscript Editor, so if you selected to put On Sale "The original .epub I uploaded" then you can skip this preview since you did not put the contents of the Manuscript Editor On Sale."
So it sounds like if you follow those steps, they will serve your epub. But there's no way for you to preview/download it to make sure except by buying your own book. I pointed out they might want to remedy that.