I found today a possible issue with integration between YARPP and Options theme (http://themehybrid.com/themes/options).
In options theme on library/functions/template-functions.php around line there is a method that automatically adds in single.php a container for related posts and automatically calls one of the following three functions if exists:
('related_posts') ('similar_posts') ('wp_related_posts')
So no matter if you check or uncheck the "Automatically display related posts?" the options theme will anyway call the related_posts() function.
This way there are cases when Related Posts appears twice in the post.
I can fix this in both ways: modifying your plugin or modifying his theme, but every custom change I make it just adds another thing to do when I update any of them.
So I see two options for this:
1. Either you modify the names of the related_posts() and the other similar methods to be something like:
2. Either Justin modify its theme to support your enable/disable function from your plugin.
Personally I would prefer the first option, which will make those methods unique and be used with any other plugin/theme.