Ubuntu – How to enable the Update notification in the Unity notification area

I don't know if this is a solution or just a workaround to your problem , but you can disable the update-notifier from startup applications. I think you will not receive anymore update-notifications then.

Open a terminal and give this command

sudo sed -i 's/NoDisplay=true/NoDisplay=false/g' -i /etc/xdg/autostart/update-notifier.desktop

Then try to disable it from startup applications and see if your problem solved.

OR

take a look inside /etc/xdg/lxsession and see if is something there related to update-notifier

A crude generic solution:

How to disable notification from network-manager.

dbus-monitor "interface='org.freedesktop.Notifications'"                \
| grep --line-buffered  'string "NetworkManager"'                       \
| sed -u -e  's/.*/killall notify-osd/g'                                \
| bash

Replace string "NetworkManager" with the desired RE to filter out messages.

To get an idea of what RE pattern match to look for run:
dbus-monitor "interface='org.freedesktop.Notifications'"
and look at the output while the notifications are popping-up.

Caveat:
killall notify-osd is non-discriminating and completely wipes the notification stack of any pending messages irregardless of whether NM is the notifying agent.

For details see:
How can I temporarily filter-out certain notification-bubbles coming from specific sources?

cross refs.:

• How to disable notification from network-manager
• How to empty the queue of pending notifications?
• Is it possible to block NotifyOSD for one application?
• filter messages to "notification area" applet
• How can I customize/disable notification bubbles?