I just installed the latest version, v3.1., on my Joomla 1.5, and the comments counter shows "0" for all my articles. I clicked on a few articles to ensure the actual comments were still there, and they are. 

I clicked on a specific article, and left my browser there for a few minutes (while I grabbed lunch), and came back to a surprise; the comments counter shows the right number for that article only.

I've got sh404SEF installed, and the default joomla "cache" option is set to off - the one found under Site -> Global Configuration.

Any tips?

I know there's something wrong with this package, because the comment counter is correct when I use a different Joomlla-Disqus plugin, RokComments (extensions.joomla.org/extensions/social-web/social-comments/6592?qh=YToxOntpOjA7czo2OiJkaXNxdXMiO30%3D)

I'll stand by.

I followed your instructions, but they didn't help.

However, I found a fix. At the moment, my website doesn't have a lot of articles. I viewed each article on the front end, one at a time. I then cleared my Joomla cache and sh404SEF URLs, and Boom! It did the trick. Now, the counter appears to be working. There are still some articles that show "0" comments, but do actually have comments. But, I suppose viewing the articles from the frontend again won't hurt, LOL!

Had I had more content, my solution would have been a pain. I hope there's something a future package can include to avoid having me have to view all the articles from the frontend.