When all three LEDs are lit up at the same time that indicates that the battery pack is fully charged. From your description, it sounds like there may be a problem with a connector or wire. We would start by carefully inspecting all of the scooter's thick wires and their connectors between the motor and controller and between the controller and batteries to try to find any signs of overheating, breakage, discoloration, or damage.
Benjamin Castañeda