Is WordPress 3.0 processing ugly permalinks - like ?p=123 - differently than 2.8.4? It's generating the ugly permalinks for the shortlink, but some of them fail to resolve & redirect - there's some consistent 404 breakage occurring for some of them.
I've disabled all plugins & removed htaccess, & this didn't help. Swapping in a copy of 2.8.4 got at least one of the links to resolve properly.
Most external links are working fine, because the normal links generated are "Day & Name."
I've checked; it's not just happening on new posts. Some of the breakage is for posts from months prior to the upgrade.