As I said, you are having issues with SIDs IMHO. I see in the picture I quoted from yours, the sid is being appended to the PM's link, which is not normal as you can see in my screens. Moreover, the extension does not sends Notifications Emails, so the Email you are talking about can only be an email that you receive if you are subscribed to the forum (native phpBB email), in any case, the links take you to the toopic, where IF you are the Host you can see the Buttons to Manage applications.
When I go to the PMs I see only my Boxes (i am the Host of the Event and logged in NOT as the Founder or admin, just a registered user)
Moreover, this extension doesn't have permissions that can bork yours.
2 permissions for standard users, 1 for admins, 1 for moderators.