OK so you have a run script executing an event which an email notification is tied to to send a notification.  Several questions:

• Do the duplicates contain the exact same verbiage or are they different?
• Do your above highlighted notification activities also fire the same event?  If so that will definitely cause the duplication and those additional notification activities may not be necessary.  Behind the scenes that activity is also executing the gs.eventQueue() API.

Just as a test, unlink one of the notification activities from your flow and see if one of them is not duplicated.