The changes to mate-indicator-applet to use the new ayatana indicators didn't make it into 18.04, and unity-panel will need changes eventually to use them as well.
I have pushed a build of indicator-notifications to the ppa which works with mate in 18.04, and should work on unity as well, but I haven't tested it yet so let me know if there are any problems.
I have also deleted the ayatana-indicator-notifications build from the repo, to avoid any confusion, so you should probably remove it.
The changes to mate-indicator- applet to use the new ayatana indicators didn't make it into 18.04, and unity-panel will need changes eventually to use them as well.
I have pushed a build of indicator- notifications to the ppa which works with mate in 18.04, and should work on unity as well, but I haven't tested it yet so let me know if there are any problems.
I have also deleted the ayatana- indicator- notifications build from the repo, to avoid any confusion, so you should probably remove it.