There are two config ID's referred to by controllers and MMS. One is MMS config ID and another is controller config ID. As the name suggests the MMS Config ID is a number which is incremented by the MMS every time the user changes configuration for a controller group in the MMS. This ID is sent to the controller along with the config file during a config push from MMS. If the push is successful, the controller sets both its MMS Config ID and its Controller Config ID to the value of the MMS Config ID that was sent in the config push from the MMS.
On the controller side, if the user makes a configuration change locally (i.e., through the CLI or the WebUI), the Controller Config ID is incremented by the controller. The MMS will detect that change, and mark that controller as 'out of sync' because now the Controller Config ID does not match the MMS Config ID. It will remain marked 'out of sync' until the next successful config push from the MMS.