In case anyone else is still having this problem, there is a fix here:
http://samdoidge.com/disqus-number-of-comments-not-showing-up-on-a-single-wordpress-post/
Around line 275 of the DISQUS plugin in disqus.php (accessible via dashboard – plugins – editor), it has the following:
} else if ( (is_single() || is_page() || $withcomments || is_feed()) ) {
change this line to:
} else if ( (is_page() || $withcomments || is_feed()) ) {
When I did this, I was then seeing duplicate "X Comments", one from WordPress and one from Disqus. Taking out the WP Comments counter in the single.php removed the code Disqus was replacing, so I ended up with no comments.
The solution for me was to add style="display: none" to the WordPress comments part of the single.php file, so it looks like this:
<a href="#disqus_thread" style="display: none;"><?php comments_number('0 Comments', '1 Comment', '% Comments', 'number'); ?></a>
This leaves the text in the source, so the Disqus Javascript can successfully replace it with it's own comment counter, but hides it from displaying to the user.