This "issue" was caused by the second XMPP client and option Mark messages confirmed as delivered to another client as read being enabled. We should not fix this as it is not a bug but having XEP-0333: Chat Markers implemented would allow us to get rid of this option and have a better solution.
Steps to reproduce:
Expected result:
Actual result:
https://www.dropbox.com/s/y5a0w9hjgre1cyz/beagleim_notifications.mov?dl=0