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I have WPMU installed on the root and buddypress installed at /wp-content/mu-plugins.
You can see the behavior by going to it: http://pedaltowork.org/
I am having the exact same problem. This is a brand new install. Here are the steps that I took:
I downloaded the latest version of WPMU (2.6.5)
I copied wp-admin, wp-content, wp-includes directories along with the files in the root installation directory to the root directory of my site.
I installed the database with no problems.
I followed the advice of the BP instructions and I created a new blog, created new posts and comments. Everything worked as expected.
I then downloaded the latest BP zip file (r598).
I copied all of the files and directories in the root directory of the zip to the /wp-content/mu-plugins directory.
I copied the buddypress-home directory to /wp-content/themes directory
I copied the member-themes directory to the /wp-content directory.
I went to the Site Admin->Themes page and selected ‘Yes’ for the BuddyPress Home Theme and ‘No’ for all the others.
Note: At this time the theme for the home page was still the default wordpress blog theme.
I then went to the root blogs (located at / according the the manage blogs page) and change the theme for it to BuddyPress Home Theme.
Now I get the 404 errors that are described above. Also, when I go to my member’s page, it says that I have no blogs, to create one. After creating another blog, the member’s page still says that I have no blogs.
I feel pretty confident that I installed WPMU correctly, but I suspect that I didn’t install buddypress to the right location(s).