It would help if you told us what version of InDesign you're using. There has been tremendous changes in InDesign's capabilities between CS5 and CC 2014.
The EPUB files produced by InDesign CS6, CC, and CC 2014 should produce EPUBs for all eBook readers except for Kindle. The method that seems to work best for Kindle is to first create EPUB, then use Amazon's Kindle Previewer to produce Kindle books.
I strongly suggest you look at Anne-Marie Concepcion's videos on creating EPUB from CS5 to CC 2014 on Lynda.com. She'll probably answer all your questions:
You can get a free week with Lynda.com videos.
Thanks for getting back to me.
For your info I am using Indesign CC 2014.