Not sure if it is buddypress related or 2.8.1, but there are a few posts about incompatibility already. I was going to try 2.8.1 myself, but as I run buddypress as well, I figured it would be smart to check here first to see what the problem may actually be.

Comments from bp forums:
1.Hi, I’ve got the members theme installed in /wp-content/bp-themes/bpmember but I’m still getting the message: You do not have any BuddyPress themes installed…. when I visit the members/blogs/groups links using the default home theme. The URLs look good.

Also, when I hover over an avatar, the URL is showing /index.php/members/jwinn and it resolves to /members/jwinn with the above error, too.

2.Hi all, did you tested BuddyPress with latest WPMU 2.8.1 (beta)? I tried it, but could not create groups and there were also other problems… Did you manage to run your BuddyPress with WPMU 2.8.1?