My top 2 heading levels, which show correctly in the Nav Pane are standard Heading 1 and Heading 2, but my third level is one I made up, Head3. I don't know whether that is responsible for the Nav Pane omitting the third level. I have three TOC's, one for
only level 1, one for levels 1 and 2, and one for all three levels. These look ok.
More clues: 1. Rt-ck on an entry in the Nav Pane and choose Show Heading Levels, set it to All. Makes no difference.
2. If I change some of my Head3's to Heading 3, those do show in the Nav Pane. But until today I had my Head3's showing too.