I ran into a problem today where notification emails were not being sent when a post status is changed from Draft to Pending Review.
I created a plugin to auto-assign a user group to all 'pending' statuses as shown here: http://editflow.org/extend/auto-subscribe-user-groups-for-notifications/
That works great. The problem I ran into is the email was never sent to the user group when a new post was set to pending. Here are the steps to reproduce:
1. Login as a Contributor
2. Create a brand new post and save as draft
3. Submit post for Review
The problem is line 324 in notifications.php $old_status was coming through as 'pending', even though the old post status was actually a draft, so the notification trigger didn't happen.
I was able to make a workaround using the ef_notification_ignored_statuses filter, but there seems to be a larger issue at play here.
Let me know if you need anymore details