I don’t think it’s a problem with the theme. If it were only a problem with the theme, I would still see the number of comments associated with a certain post in the Admin panel. If I go to my Admin panel, go to Manage>Posts, for all pre-2.0 posts, I can see in the “Comments” column, the number of comments I have for each post. For post-2.0 posts, all posts show “0” under the “Comments” column, regardless of the actual number of comments that post has. So, for some reason, 2.0 is not logging the number of comments, or is not associating certian comments with their posts.