OK so perhaps the battery's initial voltage was good, or a little low even, but if you started the bike, revved it, and the bike was shown to be charging, then there might actually be nothing wrong with the charging system at all. Remember that the most common cause is a bad battery and wiring, but if those are good, then you might have a parasitic draw. A parasitic draw is a draw on your electrical system when the bike is off, slowly wearing down the battery. You can determine if you have one by charting the fall of the voltage on a GOOD battery. If you charge it up and it is at 12.5, leave it be for 4-5hrs, come back, and see if it is lower. A difference of 0.01v or so is insignificant, but if you have dropped down to 11.5v, then you do have a draw.