BuddyPress.org

@Peter

As IntenseDebate exports your WP comments into its own system, your issue is more than likely caused by IntenseDebate misbehaving. Your best bet is to post a question on their support forums and let them help you track down the cause. I found these two related threads:

http://getsatisfaction.com/intensedebate/topics/intense_debate_comments_gone_missing

http://getsatisfaction.com/intensedebate/topics/after_installing_intense_debate_no_widget_no_comments_all_gone