Comment 2 for bug 294021

I seem to be having a similar problem on my T61p. When I boot with the secondary battery empty but the secondary still charged, I get a battery critical warning as soon as I get in to Gnome followed by an immediate shutdown. Removing the secondary battery during boot or plugging into the AC prevents the warning/shutdown and once I'm started, I can reinsert the secondary battery and charge/discharge it without problems.

I'm not sure, but this may have started when I began getting warnings along the lines of "Your battery is now holding only 49% of it's original charge capacity."

If any logs/extra info would help, I would be happy to provide them.