I really like Pages, I use it on my MBP, and on the iPad, but I wouldn't use it to create an ePub.
I don't suppose you are using a Mac, or you might consider
iBooks Author which has been designed by Apple specifically for creating iBooks.
There are also a bunch of apps on the appstore for creating books on the iPad, but I don't know how good or bad they might be.
I'm sorry I cannot help you with your particular issue... I'm not sure there is a solution, because most references I get when I use google to search, come up with solutions which involve using an application on your computer and then transferring to iPad.
Of course I may have completely misunderstood. Are you using Pages on your computer, or on your iPad, for this task? For some reason, I thought you were doing it on the iPad. If not... save yourself some grief and download iBooks Author, which is free.