Upgraded to WP 3.1 and created 2 new subsites. The admin area was fine, but the homepage showed no posts, and all new pages created gave a 404 error when viewing them. Changing permalinks to the default...no help. Thanks to other posts on this forum I deactivated all plugins and the problem was solved! Then I slowly reactivated them one by one until the site broke again. The problem plugin was A Sticky Post Orderer.