BuddyPress.org

Of course John is correct. I failed to notice that you were running BuddyPress hence my “This is truly a question for the WPMU forums” comment.

There is a constant set in bp-core.php (line 15) that allows you to set the blog ID on which BuddyPress will run. But as the trac ticket John referenced in his post indicates, setting it to anything other than “1” will currently cause issues.

Also, this ticket applies: https://trac.buddypress.org/ticket/775