Update 25th Aug. 2011: the bug discussed here is still present. I recommend all WordPress Multi Site users install the Proper Network Activation plugin that is available here at the WordPress site.
I noticed a compatibility bug between WordPress 3 Multi Site and Greg’s High Performance SEO so reported the issue to Greg who very quickly took a look at it. It turns out that WordPress Multi Site does not like it when plugins are Network Activated. So, as a warning to all WordPress Multi Site users, do not Network Activate plugins. Not yet, anyway.
To paraphrase Greg’s explanation:
When a plugin is Network Activated, WordPress 3.0 ignores the activation hook that plugins register to run whenever they are first activated. Consequently a plugin’s default options do not get set-up on subdomains when a plugin is Network Activated. It also appears, according Greg, that WordPress does not fully remove plugins that fail to setup across subdomains when Network Activation fails – the database does not get properly cleansed.
I recommend WP 3 MS users do not Network Activate plugins until the WordPress developers fix their oversight.
In the meantime, if, like me, you need to remove a Network Activated plugin that only half installed then you must delve into your WordPress database and remove its settings manually before you re-install it. Affected plugins must then be reactivated on a per site basis. For Greg’s High Performance SEO, this means you must drop the single “ghpseo_settings” entry in “wp_n_options”, where ‘n’ represents the site’s number (it will be repeated in your database almost as many times as you have sites).
In case you’re wondering, the bug with Greg’s High Performance SEO plugin was that its options could not be enabled within subdomain sites – the options screen displayed but no options could be set.
Greg has issued an update to his plugin (version 1.4.3) which addresses the installation issue but if you’ve Network Activated it prior to this update then you will need to get your hands dirty with your sites’ database. I need to stress here that the fault is with WordPress Multi Site not Greg’s plugin.
This WordPress Multi Site Network Activation bug will affect the functioning and installation of thousands of plugins. Please be careful when you activate them.
Special thanks to Greg for amending his plugin so that it works around this bug and for highlighting this surprising WordPress 3 Multi Site issue. Cheers Greg, I still highly recommend your plugin.