I just did a fresh install of Drupal 7 and I'm currently made a sub-theme with omega 3.x and for some reason the blocks page is missing the logo block. I tried also uploading a logo image on the sub-theme page and it still doesnt show up. It's very weird as it shows up on my other installs. I'm pretty sure its a basic oversight, but I'm not sure where.
Ok i found it! It seems that you need to have the "Delta" module on in order to see the "logo block" which is a core element of drupal and usually isn't on the blocks page.
Delta Blocks - 7.x-3.0-beta11 - Exposes a number of core Drupal elements as blocks.