Hi I love this system and plan to use it for an online textbook I am currently developing.
I recently tested it by posting a comment to the home page of my site with a base url like:
example.com The comment shows up just fine.
When navigating internally, however, sometimes the url becomes example.com/index.html and there are no longer any comments listed, even though the page is the same without the explicit /index.html.
Also here is a feature request -- a navigation button to close the profile view and return to the comment thread would be nice -- using the browser's back button or a page refresh is a little counter-intuitive.