Producing ePub documents from InDesign CS5.5/6 is quite different from producing documents for printing. You need to learn how to do it as it's not intuitive. I suggest you view this tutorial on Lynda.com http://www.lynda.com/InDesign-CS5-5-tutorials/to-EPUB-Kindle-and-iPad/82258-2.html
I believe you can get a free month's membership to the site.
I've been having to learn this process as well. I liken it to the old days of web development where it was difficult to get things on the screen the way you wanted to see them. There is definitely some things to learn with ePub.
I would give a +1 on Derek and Bob's recommendation for Lynda.com. An excelllent resource and where I turned when I needed help. It will teach you what you need to know to be successful with ePub's.