Just a quick note to say that the latest version of the plugin (0.3.2) seems to be resetting the query when calling wp_head(). This wasn't happening in earlier versions.
This caused an issue on one of our sites where we were modifying the main loop for a page using a call to query_posts BEFORE calling wp_head. This no longer worked with the latest version of WordPress SEO as the call to wp_head (which executes the initial WordPress SEO code) reset the query, losing our custom data. I've fixed this by moving our custom loop code to occur AFTER the call to wp_head, but thought it was worth mentioning in case other people have the same problem.