IntenseDebate seems to be having some issues with not showing comments. The comment count will be accurate, but some of the comments will not be visible. It seems to mostly affect replies to other comments.
This isn't just happening on my site, and it's not a small problem. I mean, showing your comment to other people is what a commenting system is supposed to do.
For the time being, try reposting your comment as a reply to the original blog post, instead of as a reply to a comment. I'd really rather not go through the bother of switching comment systems again, but if this becomes a recurring issue, I won't have a choice.
Edit: The problem seems to have gone away for the time being. I'll keep my fingers crossed.