BuddyPress.org

Well, that is partially true. bp hijacks the theme root and alters it to point to /bp-themes when it detects an url that belongs to the member theme. Those urls are things that are of the form mysite.org/members, mysite.org/groups …

By default it only does this for the root blog of the installation. Blog id 1.

You upgraded from what ver of bp and what ver of wpmu? wpmu now will not allow theme directory names that have a dash in them. So the non-2.7.1 theme /themes/my-theme doesn’t work anymore. It has to be /themes/mytheme

Same goes for the themes that live in /bp-themes. Did you upgrade your bp member theme and the bp home theme also?

You didn’t leave a link to your site or specify what versions of bp and wpmu you used to be running so I’m just shooting in the dark here.