Weird behavior when overriding gnome alert styling?
After installing i3 and testing with different notification daemons, It's seems that the notification you're receiving are from dunst notification daemon.
Simply removing it should fix the issue.
sudo apt-get --purge autoremove dunst
is the command you need to execute in a terminal.
Check the screenshot of dunst http://knopwob.org/dunst/screenshots.html