MU -> 3.0 Upgrade all permalnks broken

I had a WP MU 2.9.2 installation with the Domain Mapping for WordPress MU plugin running successfully.

Since upgrading to 3.0:

• any but the default permalinks 404 on all sites
• pages on any of the domain mapped blogs and the main blog 404 (including pages such as /page/2/)

• blogs not subdomained (ie those still at sub-folders) also 404 — the whole blog. It’s possible to access the admin from the admin of the main blog, but not with …/subfolder/wp-admin

have tried disabling all other plugins to no avail.

Have edited .htaccess to :

RewriteEngine On
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>

as recomended

Any ideas?