I've got a site that I'm using johnny-cache on. I have a management command which retrieves data from twitter and creates database records (via ORM) for them. When I go view the admin page for the Tweet model, I do not see new results. Disabling johnny-cache fixes this.
Since johnny-cache is applied via middleware, it seems that anything happening from script/management command will be outside of johnny-cache's knowledge and will result in stale data being served.