The battery provides Android with a voltage monitor which can only be used to estimate the remaining capacity. To give an accurate indication, you'd need to monitor the amperage, and neither the battery/phone nor the Android OS have any provisions for that. So what you're seeing is an estimate, and cannot be assumed to be a linear 100-0 scale.
Have you run the battery down entirely, then recharged it fully? The purpose of this is not to condition the battery (the new types don't need it), but to calibrate the scale. Try it a couple of times (yeah sorry, should take most of a week) and see if your problem lessens or goes away.