Have you checked Spare Parts?
I had an issue with CM6 (I forget which kernel) on two different days where when I disconnected from the AC charger within an hour it was down to 80%. I looked at Spare Parts and it showed running 100%. A reboot brought it back to normal. I don't know what was running (I had the phone next to me in the car and didn't use it at all) or if for some reason it "thought" it was still plugged in.