.. download complete.
Failed to extract source : Sub-directory wordpress-mu* was not found
.. failed! See the error message above for the reason why.
However upgrading to 3.0.1 needs some manual work.
First the file wp-content/blogs.php is obsolete and needs to be removed then you have to update the .htaccess to use the new wp-includes/ms-files.php file instead.
RewriteRule ^(./)?files/(.) wp-includes/ms-files.php?file=$2 [L]
Second the version 3.X has added a new define to wp-config.php
Which the admin will see that he needs to add when he/she visits the dashboard.
Personally there is no reason that the upgrade script needs to be used after 3.X as you can upgrade both wordpress and wordpress MU within the dashboard now. Unless you want to bug the admin to upgrade.