i m also having the same problem and yet not solved cah anyone help me.
I have installed WordPressmu 2.8.6 and its workin fine all alone now after installing plugin Buddypress 1.1.3 and changing the themes by moving the bp-themes to wp-content/themes except the home page rest all other links are showing…
The requested URL /wordpressmu/linkname(say blog or member) was not found on this server.