Okay, I took a quick look at the PDF you provided. The problem appears to be related to the fact that page 1 is a different size from the other pages:
Page 1:
/MediaBox [0 0 100.8 155.5]
Page 2 and onward:
/TrimBox [0 0 441 666]
/MediaBox [0 0 441 666]
/ArtBox [0 0 441 666]
/BleedBox [0 0 441 666]
Most likely there's a bug in Kobo's PDF implementation and something about this slightly unusual situation is triggering it. I'm not sure there's much that I can do about other than to suggest that you remove the first page with a PDF editing package like pdftk (
http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/). That might at least let you view the rest of book on your Kobo correctly.
Good luck