First of all, thank you for the super fast reply!
The issue has been resolved. It took a while for me to narrow down the cause but at the end it turned out I needed to update WordPress. All of my shortcodes on the site were displaying all post categories instead the ones that were set, I missed that earlier. I guess the newer version of WP has a different way of marking post categories and your plugin is set to work with the latest version. All sorted now. Thanks!