Okay, so I ran the epubcheck validator on the 2 books, I've renamed my book to book1.epub for confidentiality, book2.epub is A Princess of Mars from Gooogle's free e-book program. From this point on they will be referred to as book1 and book2.
Here is the output of book1, which said there were no errors.
http://pastebin.com/TbiqaHpF
Here's the output of book2, which does seem to have errors BUT works fine in the BrailleNote.
http://pastebin.com/DJdt1wgA
The BrailleNote is a Windows Mobile device that uses its own layover called Keysoft. It has its own Book Reader software as well. I know very little about the inner workings of the BrailleNote Apex as I personally don't own one. I also haven't been able to acquire any other braille note taker to determine if this is a problem with BrailleNote or a problem with braille note takers in general. The BrailleNote Apex documentation says it will play EPUB unprotected files and as far as I know this file is unprotected however I do see an encryption file in the META-INF folder, here's what it says. I tried taking this file out but no luck. Also, not all of the books we've done have this encryption file but they still don't work properly in the BrailleNote.
Thanks everyone, hope someone out there has an idea of how to fix this problem.