Sorry for the noise folks, I managed to fix it by using the current libnotify SVN revision.

Quoting their changelog:

* Fixed a bug where a notification's ID could be reset when a different notification was closed. Patch by jylefort. (Bug #94)
--
AltBlue.

In reply to Re: "onClose" for multiple Gtk2::Notify objects by AltBlue
in thread "onClose" for multiple Gtk2::Notify objects by AltBlue

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