I've just upgraded to RC4 from a copy of WPMU serveral months old. I've got everything working flawless, but for my main blog it now seems to want to force me to have /blog/ in permalinks for posts.
I've edited the "permalink_structure" value in the database to remove the /blog/ prefix, but this just changes the links on the site, and doesn't cause the pages to physically work again.
Any ideas? It worked fine on my old build :(