After an update to WordPress running WordPress MU (multisite) the root blog (ID1) went dead slow. Each request took about 1 minute! Every other site on the system was still running at normal speed.
We run a pretty complex setup with plugins like, WordPress MU Domain Mapping and Networks for WordPress (that lets ju run multiple main-blogs with it’s own child blogs).
My initial though was to reinstall WordPress and deactivate plugins and test the installation out. But no luck!
After some Google magic, I found this post at the WordPress support forums (user MacManX (James Huff)).
First step solved our problem!
1. Manually run /wp-admin/upgrade.php (visit it in your browser).
So run yourdomain.xxx/wp-admin/upgrade.php (but replace yourdomain.xxx with your own, stupid!) and run the upgrade wizard and you should be fine, if not; follow the other suggestion in the support post.
I suspect that db_version in wp_options did not match the new WordPress install.