I've just upgraded my site tonight from WPMU 188.8.131.52 to WP(MS) 3.0 and I've noticed a few things that I'm not sure if they're intentional or not. Incidentally, I'm running BP 1.2.4 too, but I don't think that should have an effect.
1. Menus: Neither Super-Admins nor regular users are able to see the "Menus" submenu listed underneath "Appearance".
2. Import: Underneath "Tools >> Import" only the Super-Admins have access to the blog importer tools. When logged as a Super-Admin I see options for Blogger, Blogroll, Categories and Tags Converter, LiveJournal, Movable Type adn TypePad, RSS, and WordPress.
But when I log in as a regular user all I see in "Tools >> Import" is:
If you have posts or comments in another system, WordPress can import those into this site. To get started, choose a system to import from below:
No importers are available.