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Usually when an electric scooter, go kart, or bikes control box (speed controller) clicks when twisting the throttle, the batteries are worn out and need to be replaced. A worn out battery packs Voltage will bounce back to a high enough Voltage level to turn the controller on, but when the throttle is applied and a larger load is placed on the batteries from the motor, the battery packs Voltage will drop down to the point where the controller shuts off. The clicking sound is from the main power relay inside of the controller when the controller is shutting off. Most speed controller will shut off when the battery packs Voltage reaches around 2-3 Volts under the Voltage rating of the battery pack.

Speed controllers are designed to shut off when they read a low battery pack Voltage in order to protect the batteries from damage due to being overdischarged. If speed controllers did not have this feature then if a scooter was driven too long the batteries would become damaged from being discharged too much.

If the batteries are over a few years old or if they sat for a long time (over 3 months) without being recharged you could assume that they need to be replaced. You could test the battery packs Voltage with a multimeter to see what its Voltage is with the scooter off, with the scooter on, and with the scooter on and throttle twisted. That type of test will tell you a lot about the condition of the battery pack. A good battery packs Voltage will be several Volts above the rated Voltage of the scooter with no load, and should drop less than 1 Volt under load.

If the batteries are new the first thing I would do is charge the batteries for a minimum of 8 hours and then follow the troubleshooting steps on this page: http://www.electricscooterparts.com/troubleshootingmotordoesnotruncharged.html