I think you have wired the batteries up wrong. Most scooters are 24 volts. the way you describe your wiring, sounds like you have wired them in parallel which will only give you 12 volts to the drive unit which will fail to power up. The batteries are normally wired up with the to batteries joined "Bat 1 + To Bat 2 -" Then the voltage across Bat 1 - And Bat 2 + will be 24 volts which will feed the correct voltage to your drive unit. Be careful to get the polarity right to the drive as this can damage the drive unit.
Bob make sure that the wiring is connected correctly to scooter controller in other words if the cables from the batteries have a connector that plug into the harness coming from the controller make sure that connectors (if color coded) match up and that they are seated correctly. Look on the underside of your rear shroud for a wiring diagram and make sure that the new batteries are wired in that way Hope this helps
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