ToC entries can be in two places:
- TOC#Inline_TOC, meaning it is an actual "page" in the ebook. The Chapter links are standard on-page hyperlinks, and have no semantic value.
- NCX, meaning it is reached from the GoTo menu. The Chapter links are defined semantically in the file toc.ncx and can be auto-generated with calibre's Edit ToC, if all chapter headings within the ebook are wrapped in the h1/h2/h3/h4/h5/h6 HTML tags.
One way to create a working, valid ToC is to open the book in calibre's Edit Book feature (shortcut key is "T") and edit the HTML code by each "Chapter $$$" header, to be enclosed in the
Code:
<h2>header goes here</h2>
HTML tags. Then use Generate ToC and it will find thse headers. If your book is not finding the chapters properly, it is probable that the header tags are missing. If you converted this book from a PDF, then I am guessing this is the problem.
For future reference, PDF is a horrible source format to use (as detailed in this sticky:
Read this before Posting PDF Questions), and should only be used when there is no other choice. You must expect them to need special treatment.
It may be worth reading this sticky as well:
Chapter Detection/Table of Contents Tutorial.