Ryan, my analysis is not incompatible with your problem.

The positioning logic in notify-osd is not very sophisticated and
TwinView, which the developers may not have been able to perform
substantial testing under, introduces additional complications. One
problem, which I described above, will occur if and only if there is no
GNOME panel at the top of the screen. As you still have the top panel
then you are experiencing a different bug arising from similar logic.

I like your idea, Oli, although I am not sure if there is a reliable way
to query the GNOME desktop to locate the notification area. The method
for locating just the panel is rather cumbersome, albeit reasonably
reliable; each window on the desktop is iterated in an attempt to match
one with a specific class name. Perhaps the maintainers can think of a
way?

(There are additional structural problems in notify-osd which would need
to be resolved to position the OSD at lower parts of the display. e.g.
The height of the bubble is not currently known when the positioning
logic is invoked, because it is not required when the bubble starts at
the top and grows downwards.)

-- 
regression vs. notification-daemon: positioning when multiple screens are 
available
https://bugs.launchpad.net/bugs/331369
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