I've identified more about the problem, but still no solution.
The issue lies in the multiple page layout feature of TT and here's more detail on the bug:
I have a home page template with no sidebars, but an interior page with 2 sidebars. When I load the template, the option to turn on or off the sidebar navigation goes away. Theme Options is using the home page to say "there are no sidebars, so we don't need an option to turn off the sidebar menus" even though the interior pages all use a sidebar layout.
Only by loading a template that has home page sidebars do I see the sidebar menu options in Theme Options as mentioned by Sarah.