I guess because the first or the second instance has the “Show the plugin under content” option enabled. That way the plugin is automatically placed under the content.
Here is a detailed explanation of it in the documentation: http://wp-relatedpostspro.demo.wp-dreams.com/docs/#getting_started_placing_the_instance_to_the_frontend
If you turn this option off then it will be visible only on pages where the shortcode is placed.
There are also chapters about how to override the visibility with metaboxes. Please go through quickly the documentation, it has answers to most of the questions you posted.
Best,Ernest Marcinko
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