I'm having a similar issue with a merged HTML5 project, though I see different issues with different browsers. The project is downloaded from our server locally onto the client's computer so the project is accessed locally. Using Azure_Blue.
In IE11, the parent (TOC, index, search, etc) is recognized and works properly but links within the topic do not work unless they're opened in a new tab.
In Chrome, the navigation continuously loads and eventually freezes the page.