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?
Well, we got a couple of options here.
1) hack the theme and git rid of the content div in the header.php. That means changing all existing templates that rely on that content div being gen’ed before it gets to them
2) hack the directories and all other code that just assumes that they are responsible for gen’ing their own content divs and leave the theme header.php alone
3) get a different theme