It seems this has been reported and partially diagnosed upstream:
http://bugzilla.gnome.org/show_bug.cgi?id=361583

Based on that upstream bug's discussion and my own reading of the g-p-m
source code, I am confident that my problem is not related to ACPI: it
is clear from the g-p-m source that when all battery events are being
generated properly, it will still trigger a critical low power shutdown
if any one battery becomes empty, even if other full batteries are
present in the system.

-- 
Dual / Two Batteries, shutdown on empty expansion battery. (GPM does not 
recognises second battery on hotplug)
https://launchpad.net/bugs/60442

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