BuddyPress.org

Maybe I am wrong, but I think I read somewhere that BP needs you to change the link structure to anything but default.

In WP Mu you do that in a box that looks like in WP. You just have to scroll all the way down to Settings->Permalinks. You can copy and use this link when you have changed your-domain.com to the domain where your WPMU is. : http://your-domain.com/wp-admin/options-permalink.php

If you have no clue what to put in the field I would suggest: /%category%/%postname%/