Yeah, this is weird. I did a fresh install on a test site for giggles. Installed WordPress, then installed and configured All In One SEO. Everything worked fine. Metatags and description showed up fine.
Then I installed atahualpa with the SEO option turned off and my metatags and description disappear.
Switch back to the default theme and the metatags and description show up again.
I have the <?php wp_head(); ?> function in the header.php called before </head> so I’m not sure what else is going on here.