I also have noticed this as well. SPB Mobile shell and the SPB Pocket Plus Battery meter have shown that I have more battery than windows mobile states.
So today, I have let my phone die completely - it will not turn on, and have been trying to charge it with the USB cable. (I was trying to reset the battery status so that it knows when it is fully discharged) It will not charge through the cable at all. I am wondering if it has to be on to negotiate something with the USB to charge it. Not sure, but at least I know not to run the battery completely down if I don't have the AC adapter.