Comment 187 for bug 403135

I believe this bug is somehow related to a change in gnome-panel_1:2.29.5.1-0ubuntu1 when the building of applets as shared libraries was deactivated (they are now build as standalone executables)

Changelog: http://changelogs.ubuntu.com/changelogs/pool/main/g/gnome-panel/gnome-panel_2.30.0-0ubuntu1/changelog
* debian/rules:
    - don't build in process applets during the unstable cycle so crash issues
      should be easier to debug and reported on the corresponding binary

It seems to me that due to this change, the notification area icons get the background of the program's main window instead of the panel's background.

Compiling gnome-panel with '--with-in-process-applets=notification-area' in debian/rules (and no other changes), fixes this bug for me.

I have uploaded modified gnome-panel packages to my PPA: https://launchpad.net/~cyfex/+archive/ppa in case others want to try this (you need gnome-panel and gnome-panel-data; killall bonobo-activation-server and gnome-panel after installation)