There are some compatibility bugs between WordPress 3 and some plugins, for example Greg’s High Performance SEO plugin, under the Multi-site mode. Multi Site was formely known as Multi User in previous versions of WordPress MU, and is activated by creating a network of sites under one WordPress installation.
As can be seen on the WordPress Plugin Repository, WordPress 3 has problems initializing plugins properly. This could potentially affect the functioning of very many plugins and therefore it is advisable to all Multi Site users not to Network Activate plugins until this bug is fixed.
Usually when a plugin is first activated, it registers an activation hook which will be ignored by WordPress 3 if the plugin is network activated. Therefore the default options of the plugin do not get setup on subdomains.
Unfortunately, plugins that do not get setup across subdomains when network activation fails, are not fully removed by WordPress and so the database does not get fully cleaned out. This means that if you need to remove the plugin you must also remove its settings in the WordPress database before re-installation.
Come on you brilliant WordPress Developers fix these issues fast so that (nearly) the whole world can continue to be productive using (probably) the most influential open source application ever!