I contacted Joost de Valk (Yoast) via his site and asked if he is watching this post with info about it. Hopefully he will reply here soon.
BTW: I updated to WP 3.3.1 today and still have the same problem on Blog pages:
The SEO title does not replace the WP title, and the meta tags and canonical link do not show up, although the comments normally surrounding them do show up. All other pages are fine.
Also my “two titles” showing up on all pages seems to be resolved (not sure why) – perhaps this was not related to the SEO plugin.
Nick