Question on publishing to executable

We have a course whose main menu is a Flash menu, that links to each chapter in the course. After publishing to "Single file executable" and running it, when we click the links in the Flash menu, instead of opening in the course viewer, the links are opened in the user's default browser. This doesn't work, because the browser is just sent a page name, no path information.

I also tried adding a javascript menu we've developed to look like the Flash menu. However, Lectora won't publish for executable or CD-Rom with it in the course because it's "External HTML".

So I'm wondering, what's a good way to develop a custom menu that will work with Publish to Executable or to CD-Rom?