I upgraded to WordPress 2.0 a few days ago. I just noticed today that the comment count isn’t incrementing when people post comments (although they do decrement when I delete a test comment). So there’s all those posts on my main page that say “Comments (0)” even though they have comments. And they’re not showing up in my “unread comments” plugin either.
I think I’m going to have to try turning off some plugins to see if that makes a difference. I hope it’s not SpamKarma.