I emailed ctek - they replied that the charger should be disconnected from the battery before starting.
As the perminate attachment leads are only short and I don't want to have to lift the bonnet everytime I start the car so I guess I'll have to use longer leads and/or a clever relay arrangment.
Are you able to route the permanent leads through into the car ? so the charger can be disconnected from the battery and mains supply before starting!!