calibre's FB2 output creates on section for the entire book. While this is valid, creating individual sections for each chapter is preferred. Most FB2 readers will auto generate a TOC from the individual sections within the document.
Due to incompatibilities (not limitations) between the FB2 format and how calibre handles chapters creating sections for each chapter is near impossible.
FB2 uses the text from the chapter itself:
Code:
<section>
<title>
<p>I am what will be used for the TOC as well as the chapter header in the document itself</p>
</title>
<p>...</p>
</section>
...
calibre has a very flexible TOC generator which can create TOC items from text, and tags. TOC items can have different text than what is contained in the book. Also, TOC items can point to location not just content. This works fine with XHTML which calibre uses internally during conversion to represent the book. However, there is no good way to convert something like the following to FB2 while marking the chapter properly.
Code:
<a id="toc_1" />
<div>
<p>The toc_1 has different text than me. I'm in a p but I could be in pretty much anything. I could even be something like <p><b>Title</b><br />Start the text.</p>
</div>
Basically there is no good and reliable way to turn that anchor point into a proper FB2 section. We can't use the text from the TOC item itself because we don't want to modify the actual book content. We also can't reliability tell what to include in the <title> tag of the section.