Add Semantics won't update the Landmarks section in your ePub3. You'll have to manually add them to the nav document. At a bare minimum it should look like this:
Code:
<nav id="landmarks" epub:type="landmarks">
<h2>Guide</h2>
<ol>
<li>
<a epub:type="cover" href="../Text/cover.xhtml">Cover</a>
</li>
<li>
<a epub:type="bodymatter" href="../Text/chapter01.xhtml">Start Reading</a>
</li>
<li>
<a epub:type="toc" href="../Text/nav.xhtml">Table of Contents</a>
</li>
</ol>
</nav>