Most topics missing from Contents/Index when I compile for HTMLHelp

I write and maintain two Help systems using RoboHelp. One compiles fine for WinHelp 4, HTML Help, or WebHelp. When I compile the other system, however, I get all topics only when I compile for WinHelp 4. If I compile for HTML Help or WebHelp, most topics are missing. The only topics that appear are glossary topics and links to my company's web site. The one distinction I can make between the two systems in terms of features, not content, is that the one with problems compiling uses a "See Also" button in all the topics that aren't appearing (the glossary topics and web links don't include a "See Also" button). The system without any troubles compiling doesn't use a "See Also" button at all.

I will be eternally grateful for suggestions on how to resolve this issue!