At the output connector of the charger, you should measure very similar to the specified output voltage.
Unless you have modified software for the charging controller, which I can imagine would be difficult, it is probably a hardware fault. The controller will interface the processor, battery and power input to stop charging when full, to prevent overload or overcharge, maybe have a low voltage disconnect - stop discharge when batteries get too low.
Maybe start by visually inspecting the controller, which should be close to the input connector, for any burnt or bulging components?