Make sure you copied the up-to-date universal embedding code directly from disqus! The important part being the “//” prefix to the shortname (instead of the full “http://” Otherwise, you’ll get a quiet mixed content error and the comments section won’t display.
A lot of examples out there will have embedding code you might copy, and many of them were done before github pages supported https (summer of this year.) I saw some people out there with unresolved questions asking why there disqus wasn’t working, this could be one reason.
-chris