Hmm, actually, no I have updatd to 2.0.4 and when I deactivate my SEO plugin where I had made the above mods that addressed the canonical bug, I return the former situation where the canonical url is set to the url of the first post in the list. As soon as I turn the SEO plugin back on, the canonical URL switches to the one I had set there.
Maybe the plugin links reported by Will were fixed? From what I see the situation remains the same on my site.