BuddyPress.org

@modemlooper, if you are changing from one permalink structure to another then the .htaccess file has to be rewritten by wpmu. You should be able to run any permalink struct you want. When you modify the permalink structure make sure you temporarily change the directory that contains your .htaccess file for wpmu to 777 and then make the change. Change it back to something safe afterwards.

If wpmu thinks you have permalink struct A and .htaccess is setup to handle B then you get problems.