I have WP 3.4.2, WordPress SEO 188.8.131.52 and Buddypress 1.6.1 - I'm also running latest BBPress (in compatibility mode, theme is injected in the template's page) and Buddypress Template Pack 1.2.1 which helps loading Buddypress into the current theme
I noticed that Buddypress was loading contents of the header.php twice (most likely firing wp-header() twice), the second time inside the 'body' html tag and thus resulting in duplicated metas, scripts and stylesheets. For some reason it's not loading properly the wp-footer() either, the footer.php appears truncated just before that.
I'm not entirely sure if WordPress SEO was the cause of the problem, however as a matter of fact after I deactivated it, the header duplicate was gone. I will send a message also in buddypress forums notifying the issue.