Moved to InDesign EPUB forum.
You need to tag the paragraph style you are using for the chapters in Paragraph Style Options/Export Tagging/Split Document (EPUB only).
Ok, I hadn't tested the advanced options out in the export menu. It works and does so on both the iBooks and Kindle previewer.. which is good news since that is really important to me to try and find a workflow I can update both of these formats from when I continue to work on my book.
The only strange part is that on some chapters its adding an extra blank page between the chapter and the next. What is odd is that it only happens on some of them (in the iBook reader only, the kindle previewer isn't doing this)
I am going to look into this more closely but its not a major deal as I would prefer a little seperation in the chapters anyways, its not really a bad thing. It is just hard to figure out why its doing this.