A while back, we switched to Disqus for commenting. We've had a very good experience so far, and outside of a few individual issues, it's helped discussions move along easier than our previous commenting system.
I know many look at the home page and other index pages for the comment counts on stories, and they've all been listed as 0 since April 2nd, no matter how many comments have been made.
I had let it be, because I thought it'd be a quick fix, but as this is taking longer than expected, I have removed the comment counts to prevent confusion. When the issue is resolved, I'll put them back.
In the meantime, know that all comment counts below the story and above the comments are correct. It was only outside of the story that there are/were issues.