Captiv8r I was experiencing the same problem as thread #TOC Navigation pane doesn't show in WebHelp Rh2015 , however, when I generate my WebHelp (in RH 9), "....index.html" isn't trucated on my start page file name, and appears correctly prior to publishing. Only when I publish to SharePoint 2013 does it hide the TOC pane. The "Show" link isn't visible on the start page - just the start page that doesn't have any links for the user to navigate. Can you perform your magic for this one?
-Danni