BuddyPress.org

wp-admin? Why do you need to access it from BuddyPress? BuddyPress is designed and developed, so users won’t have to go to standard wp backend to configure and use the site, unless they have their own blog.

Anyway, all upgrade should be done manually (by FTP or SSH?). If you think your install is buggy, try reinstalling.

btw, have you set correctly so that new theme architecture to work?