When running on a site using https, popups will not work at least under Chrome unless you load unsafe scripts. I was able to get around this at least on one page by changing line 24 of templates/home.tpl to use https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js rather than http
Changing src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"
to
src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"
in all the .tpl files in ./templates
seems to fix the comments not popping up (and makes the Admin menu work again)