Yes, I have had the same experience but have not yet figured it out.
I strongly recommend learning to create EPUB using one or both of these resources:
(1) eBooks by Elizabeth Castro at her website:
(2) Videos by Anne-Marie Concepcion on the Lynda.com website.
Creating EPUB files requires some extensive learning, and it's very difficult to do it on your own.
When you convert ID to epub, the program follow the order of the text/frames.
If your frames are linked, any other frame that are not linked, even if it are in the page 1, will appear after the linked frames.
I recommend break the links before the Contents section to make appearing in the correct order that you want. This applies also anything that you want ordering.
In epub, to break it in pages separetely, the prodecure is different, you have to break in files or indicate the paragraph style on convert section.