The root element is most likely the cause for the error when batch checking. Try removing the root element parameter in the .json files manually to see if the plug-in inherits the correct extraction settings.
Please keep in mind, if you are batch checking more than one document type simultaneously, concept, reference, topic, task, etc., it could be that the plug-in is not able to choose the correct extraction settings as it can typically only use one extraction setting at a time.
If this is your scenario, try batch checking groups of document types at a time (concept, reference, topic, task, etc.).