I have a problem with N900 battery charge, too. I had BatteryGraph installed, I purged it, this strange problem didn't change.
Facts: the battery-status hildon-menu indicator can show you red battery and "Battery low" notification when, according to bnf, the battery charge is about 30%-50%. And, after leaving the device turned-on, cellular-radio-on, wifi-off, no-windows-open, no-charging, no-usb, no-bluetooth, no-GPS... The battery indicator returns to normal, bnf-compliant, green value. And this nerves-destructing event can repeat itself several times during one short trip. I don't know the reason. I can only thank bnf for supplying me with plausible information.
Best wishes.
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Per aspera ad astra...