I suspect this is a WordPress issue from the most recent update, or maybe a plugin issue, but thought I’d check. Since the most recent update, commenters who try to reply to a previous comment don’t get threaded, but added as a new first-tier comment.
While we’re on the subject of comments, I was looking through hooks to see if there were any to add into the comments section because I wanted to add an option to opt-in to a newsletter. Didn’t see any hooks but wanted to make sure I wasn’t overlooking anything.