At the top of iBooks app you can choose between Books, Purchased Books, and PDF. Have you made sure it's not set to purchased books? Failing that I would use an online ePub converter, even though your file is ePub to begin with ... just run your file through it to make a new ePub and try to sync that file instead. Also double check in iTunes that your particular book is checked off..sometimes it is set to sync selected books and the one I want to sync does not have a check mark.