I don't have duplicated activities for sure. I checked once more. When auto update is off, every item is displayed just once.
I'm think that problem is with Auto Actions. I see that you've made some changes lately so I used "Reinstall System Actions" and unpublished all my Actions and turned on auto update feature.
All old activities are displayed just once.
New (and old one with new comments) are doubled after comment is added - I see the (I think) original one, and additional with "log?"/notification. In original item, comments are displayed twice and I don't see menu in top right corner of entry.
In doubled items I see comments displayed once, with menu in right top corner.
If you will have couple of minutes I can add a user to front end for you.
Everything looks a little better that some time ago. Lets look at the screenshots:
1. after comment is added by test user
notification is displayed, which is cool but if, it is possible, it would be great if source post could be displayed at the bottom at once with this notification and with new comment under the post (everything without refreshing site).
2. after refreshing a site
source post is under notification, there is the new comment, and I like it (but why only after refreshing site? ;( )
and there are two the same posts - with notification and without. In this without notification comments are doubled.