When low on power, the Notification icon seems to flicker when it appears. It also appears every 30 seconds or so, which feels way too frequent. Additionally, I have the compositing manager 'on' in xorg.conf, which means that it's trying to draw it with an alpha channel, etc.
Could you provide the output of the "gnome-power-manager --verbose --no-daemon" log please when the flickering appears please. I can't reproduce it here.
I've reworked the icon handling this weekend. This should fix any problems you had with the icon, as I managed to reproduce the flicker you mentioned. The fix is in CVS.