If the F5 config uses partitions, this activity does not output any of the configuration in those partitions, only the base config.
This was raised a while ago (2014) as an issue with NCM, so it may be you have a fix in that product which could be used?
OK I have found the answer and I can do it with a variation. If anyone else needs to do this, change the "show running config" command to "cd / ; list all-properties recursive"
Works a treat.