The plugin checks the path of each installed plugin against a list of those for plugins not in the Plugin Directory and if the path is on the list it then checks to see if the plugin is currently not in the Plugin Directory before listing the plugin as no longer in being in the directory, so what you are describing wouldn’t normally be possible.
The only thing we can think of is that something else on the website is modifying the data coming from WordPress about the plugins, which is used for those checks. If you can point to something specific that causes the issue to happen, maybe a certain plugin being installed, we can further troubleshoot this.
