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There are two possibilities.
The first is that NP's Manuscript Editor (which is buggy) has garbled your EPUB file.
The second possibility is that your EPUB file was buggy when you submitted it, but Calibre's E-book Viewer was able to work around the bugs. You haven't mentioned running your EPUB file through EPUBCHECK, which is required by Pubit and by the iTunes Bookstore. Have you done that?
Have you attempted to upload the .doc file directly in NookPress?