Hi. This is just a thought but have you tried putting the batteries back on the scooter and putting a volt meter on the batteries to get a reading when the lever is pressed on the scooter. Batteries can display as being fully charged (+12 volts) but often fail under load, meaning that as soon as you press the lever, the voltage will drop right off. If this happens, it is more than likely that your batteries are to blame.
Hope this helps.