I ran into a similar problem (bug 120258) with incorrect discharge time shown.  
For that, it was resolved as follows:
In gconf-editor, set apps->gnome-power-manager->use_profile_time to FALSE 
(unchecked).  

It was reporting my discharge time as much less than real (55 min
instead of 4+ hrs), and after the 55 min passed, I started getting
notifications similarly to what you described.  After applying this
gconf change, the popups went away.

Could you check and see if doing this resolves your bug as well?

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