Plugins have limited ability to hide/show to built-in UI elements - they can hide/show the inventory bags, party display, plugin manager, target display, and player vitals display.
As to plugins hiding/showing themselves with the UI, the answer to that is a bit tricky. There is no way to programmatically detect the current UI state (displayed/hidden) so plugins rely on detecting the Hide/Show UI actions and the Esc/Cancel action - plugins aren't allowed to detect actual key strokes, only action codes which can be triggered in a number of ways. So, most authors default to the assumption that the HUD is visible when the plugin is initially loaded (which is true if the plugin is set to autoload on login in the plugin manager) and then hiding with the Hide UI action or Esc key and showing with the Show UI action/plugin command. If any of these events occur oddly, such as using a command to display the plugin while the HUD is hidden, the plugin will get out of sync and display oddly until it is unloaded and reloaded. If you are seeing other behavior with a specific plugin, you need to post that as a question for the plugin author, typically in the download page for the plugin here at lotrointerface.com. I would not recommend altering plugin files directly yourself unless the plugin is no longer being updated or the author directs you to since any changes you make will get overridden by any updates in the future. It is preferable to get the plugin author to fix the plugin or let you know why you are seeing the behavior you are.
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