I've written a brief blog article at http://www.dansmart.co.uk/2012/01/setting-the-meta-description-in-the-all-in-one-seo-plugin/, which says the following. Hope this might help some people.
A little tip to save you the time it took me to work out what was going on with the All in One SEO plugin for WordPress, and why a site I recently converted from static to WordPress lost its Google ranking for a while. Each page had an optimised title and meta description, yet when I googled the site, the meta description wasn't showing up in Google.
With the All in One SEO plugin, you are able to set an optimised page title, and a meta description. This is done from the Edit page screen for the pages in question. I'd set this information for the Home page (which was a static page), so why wasn't it shown up?
It turns out that the All in One SEO plugin doesn't use the title and description set on the 'Home' page's Edit page screen, even if it's been set. Instead it looks at the Settings -> All in One SEO page instead, which has two fields: 'Home Title' and 'Home Description'. I would argue that this is not an obvious place to store this information, and that the plugin should be implemented to look at the Home page's 'Edit page screen' details, if it's not set here.