You've probably done this, but I would make sure everybody has checked their outbox and deleted items for the phantom messages. While I can't say I noticed anything with the new version, emails disappearing has been a chronic problem for us.
While it's nice to be able to "retract" a message from your outbox, this functionality isn't worth the lack of message tracking. It would be nice if the format were similar to outlook or other email clients, so if somebody doesn't get an email, you can always find a copy of it in your sent box.
