I know from flying R/C aircraft that LiPoly batteries can be hard to measure. Old school batteries (NiCad/Nimh) have a nice linear discharge curve.
If the NiCad battery has a max of 6 volts and is dead at 0 volts then at 3 volts you're half way through. With Lipolys if it has a max of 6 volts it stays pretty close to that until you're most of the way through the charge then it drops off suddenly towards the end of the charge.
Because of this LiPolys are hard to measure. The only accurate way to tell is to watch the current draw over time (Milliamp hours). The other issue with LiPolys is if you discharge it to 0, it's toast. You can only discharge them to a certain minimal voltage.
So, I assume after a battery pull your phone is making a best guess based on voltage. I know on my old original droid you had to calibrate the battery reading by fully charging then discharging the battery in the phone if you wanted an accurate reading.
Hope this helps and doesn't just confuse the matter.