I had this issue with the extended battery as well. Just guessing here, but I think the incorrect readings have something to do with the batterystats file in the OS not being properly calibrated.
The issue went away when I drained the battery to empty. Plugged in the charger and the led was blinking red. Turned the phone on as soon as the led went steady, and did the standard bump charge deal.
Since I don't really know the cause of he problem with any certainty, I can't be sure this isn't shooting in the dark. But everything I've read so far seems to indicate the possibility is there.