404 Errors on MU to WP3 Network Upgrade

Up until recently, I was running a WPMU 2.9.x installation in subdomain mode. Yesterday, I applied the 3.0.1 upgrade through the dashboard. The suggested edits to .htaccess and wp-config.php were done–and everything appeared to run correctly. Until…

I created a new blog, and went to edit the |About| page. The new title appeared in the theme tab, but when clicked on returned a 404 page. Checking further, new posts appear correctly on the main index page–but when clicked on for a “read more” or single page display create a 404 page instead.

Going back to the main blog, all old posts also display properly on the main page, but again any tab to a static page or single page display by clicking on either “read more” or the article title returns a 404. Here is the .htaccess, but I find nothing wrong:

RewriteBase /

#uploaded files
RewriteRule ^(.*/)?files/$ index.php [L]
RewriteCond %{REQUEST_URI} !.*wp-content/plugins.*
RewriteRule ^(.*/)?files/(.*) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^.*/wp-admin$
RewriteRule ^(.+)$ $1/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule . – [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-.*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]

<IfModule mod_security.c>
<Files async-upload.php>
SecFilterEngine Off
SecFilterScanPOST Off
</Files>
</IfModule>

Clicking on anything that directs away from the index page goes 404 in the existing blog or a newly created one. As I say, this was running fine until the upgrade, with no issues on new created or old blogs.

Any suggestions, as the site is pretty useless now…

P.S. URL is