I've found what I think is a bug in Mark Jaquith's superb Subscribe to Comments plugin.
He has been looking into it (ticket here: http://dev.wp-plugins.org/ticket/620) but has yet to see the problem. In short, Specifically the new fancy Ajax comments page (/wp-admin/edit-comments.php). When you approve comments that are pending moderation, no emails are sent out...either to the author of the post or the subscriber/recipient.
Anyone come across this or know what might be causing it? It seems to me like the plugin is being ignored. Approving comments from the "moderation" panel is fine.
Having checked his blog, it seems he has just lost his sister, tragically, at just 13 - so now is not the time to be mailing him about a stupid plugin. Thoughts to Mark and his family at this dreadful, confusing time.