1Section heading not showing up in PDF

What typeface/font is being used for the text that disappears? With FM's SaveAsPDF route with the CMYK option some fonts do not render properly (i.e. they either disappear, go white/invisible or use the incorrect metrics). It usually doesn't happen using the RGB route, but there are other settings (in the joboptions file - Settings > Fonts > When embedding fails - should be set to Cancel) that could affect the output. So which joboptions file did you use?

Is the AdobePDF the default printer instance when you are creating the PDF from FM?

In the PDF, check to see if there actually is any content where the missing TOC entries are supposed to be, i.e. try a text selection (and copy & paste into a text editor to see if the content is there but invisible in the PDF). Also use the Link tool to see if there is a link area surrounding the missing text.