What is the title/author of the book? It's likely that a sample would show the same issue to make it easier to troubleshoot.
Your comments suggest that it is not a kepub but rather an ePub. If you open it with Sigil or calibre's ebook editor, do you see the mass of Kobo spans that you should?
The spans will look something like this:
Code:
<span xmlns="http://www.w3.org/1999/xhtml" class="koboSpan" id="kobo.1.1">
Near the start of each file, you may also see items such as:
Code:
<!-- kobo-style -->
<script xmlns="http://www.w3.org/1999/xhtml" type="text/javascript" src="../js/kobo.js"/>
<style xmlns="http://www.w3.org/1999/xhtml" type="text/css" id="koboSpanStyle">.koboSpan { -webkit-text-combine: inherit; }</style>
You can also try running the ePub through kepubify or using the KoboTouchExtended driver from calibre.