In case this helps, I found that I had the same problem upgrading to 3.1 as I did for 3.0, namely, the back-end area is incredibly slow.
For whatever reason, I have to access /wp-admin/upgrade.php manually for every blog on my network.
Disabling all of the plugins and removing the admin bar didn’t help. But once I actually upgraded the databases manually, everything was peachy-keen. Now if I can only get my sysadmin to upgrade the server…