Noting everything in one issue for now. (Please let me know if you'd like me to create separate MDL issues.)
1. Messages not being marked as read - I mistakenly ticked all boxes in destinations for incoming messages and now have a long list of messages (copies of forum posts and IMs) which refuse to go away.
2. Jabber is not working as a destination for incoming messages.
3. Email copies of IMs have title "IM" and no indication that they came from moodle.org. Could you add a sentence at the end of the email as done previously e.g. 'This email is a copy of a message sent to you on Moodle.org http://moodle.org/message/index.php?popup=1'.
4. Messaging settings for each user on upgrade are not the same as previously i.e. sending email copies of IMs.
5. Maybe I blinked and missed it, however I have not yet seen a messaging popup.