Howdy. The plugin-template.php is used when you are running a non-bp home theme. As far as I can see it’s the only time it’s ever used. The plugin-template.php calls get_header(), triggers an action ‘bp_template_content’ and then calls get_footer(). Whatever is triggered by the ‘bp_template_content’ event, renders the stuff in between the header and the footer. The content div with the groups directory stuff inside it in the case you mentioned.
If you are getting two content divs then your theme is starting a content div in it’s header.php file. Gotta be. That should be left to the rest of the theme’s template files.
Am I understanding what you are saying?