As Donncha explained it in his post upgrading to WordPress Mu 2.9.1 needs special attention otherwise you’ll probably get errors due to a missing new table in the database.

• Your website must be running under WordPress Mu 2.8.6. Should this not be the case, upgrade manually to 2.8.6.
• Before you upgrade to WordPress Mu 2.9.1, download add-commentmeta.txt and rename it add-commentmeta.php
• Put the add-commentmeta.php file in the /wp-content/mu-plugins directory
• In the administration area, go to Site Admin->Upgrade in order to upgrade all blogs. This will run add-commentmeta.php which will create the missing table for all blogs on your site. Let it run, it may take a while.
• Now upgrade to version 2.9.1 manually or via Tools->Upgrade menu
• Delete the /wp-content/mu-plugins/add-commentmeta.php file
• Repeat the  Site Admin->Upgrade operation in order to upgrade all your blogs.