I am using two monitors on my system, with a height difference between their resolutions. The monitor on which the gnome-panel appears is positioned lower on the virtual screen. As a result its top left screen co-ordinate is (0,48).
The nett result is that "_window_look_for_top_panel_attributes" in src/defaults.c:2408 is unable to find the gnome-panel to position the bubble relative to it, as it expects the panel to be at (0,0) not (0,48).
Secondly "defaults_get_top_corner" in src/defaults.c:2530 miscalculates the top position of the bubble when the gnome-panel is not at (0,0). As far as I can tell, panel_rect.y (retrieved from gdk_window_get_frame_extents) already includes the offset defined by rect.y (retrieved from gdk_screen_get_monitor_geometry).
Hopefully the attached patch makes things clearer.
still in progress :O ?