Well, I click a button that says "View Primary Layout" when I mouse over it. And when I do, it says "This only works if you've generated it, do you want to?" and I click yes and POOF, up comes IE with my files in it and nothing in the navigation pain.
I don't see anything separate that says anything about generating a Table of Contents. I can't even find a Table of Contents pod (referred to in Help) in the View > Pods list.
I have a Table of Contents folder in the Project Manager, but I don't think that qualifies as a pod.
In Project Manager you should see Table of Contents listed. From what you say, instead of setting up the default TOC, you elected to create a new one. That will be confirmed by you seeing two entries under Table of Contents.
Then probably what happened is instead of setting the wizard to use the new TOC, you left it with the default so you generated using the default instead of the TOC you had created.
Double click the Primary Layout and change the TOC used in the first page to your new one and it should be OK.
If you double click a TOC in Project Manager, you should see it open in a pod.
See www.grainge.org for RoboHelp and Authoring tips
I didn't see a table of contents on my first try, so, yes, I created entries and used those, though they didn't appear when I generated the primary layout.
So I started over with a new, blank project and figured out that if I click on an entry in the Table of Contents folder in the Project Manager, it opens the TOC pod. It looks like we're good there, except that it generated the TOC in reverse order (they're numeric entries, 4.5 is the highest one and 4.1 is on the bottom).