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https://bugzilla.redhat.com/show_bug.cgi?id=529920
--- Comment #4 from Matthias Clasen mclasen@redhat.com 2009-11-25 20:46:18 EDT --- You could either
Always place the panel on the primary monitor. See XRRGetOutputPrimary(), GTK+ api for this will be available in 2.20 before the end of the year. This is what the gnome-panel does (or at least tries to do).
or
Make the panel jump to the monitor which contains the active window. See things like gdk_screen_get_monitor_geometry() and gdk_screen_get_active_window() for how to get the necessary information.