Bruce Cowan is correct, the 03_fix_xinerama_stack patch introduces this
problem, however upstream still has the problem that that patch is
attempting to fix.

I have attached another patch that attempts to solve both problems.
It's still not perfect; ideally we would like the default monitor to be
the one the notification applet is on, as that way the notifications
follow the notification area, which makes sense.  Unfortunately this is
not easy to determine.

** Attachment added: "Replacement patch for 03_fix_xinerama_stack"
   http://launchpadlibrarian.net/22762989/notification-daemon-0.3.7-mbt2.diff

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Notifications overlap the bottom panel.
https://bugs.launchpad.net/bugs/45544
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