Question

"I have a problem with the content menu that is automatically generated.  The contents menu data that is extracted from the PDF on the fly does not reflect the contents menu that I have set up on page 2. Two section headings are missing.  It is missing links? What i’m doing wrong?"

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Solution

I took a look at the PDF sample that you forwarded and i spotted the issue. While you have set these 2 options up as links to pages within the PDF, the reason that 3D Issue is not detecting them  is because those options are not in the PDF’s contents menu. This can be seen by selecting View->Navigation Panels->Bookmarks from the menu in Acrobat reader.