I update my WordPress Network quite often. Especially to prevent security issues. Load time for typical WordPress pages is as good as perfect. However, I discovered on some of my WordPress Network setups the wp-admin pages suddenly took forever to load. I was waiting 2 minutes to load any wp-admin page. After a long search I discovered the problem was a faulty db_version value in the wp_options table.
I usually auto update my sites and found out this value was not updated (or could not be updated automatically).
WordPress Codex pages (http://codex.wordpress.org/Version_3.6) list this value for every WordPress version. For example: Version 3.6 has database version 24448. Thus, you should update this value manually in your mySQL database: change db_version (option_name) in wp_options to 24448 (for version 3.6). You should repeat this for every site in your wordpress network (wp_2_options, wp_3_options, …).
It’s as ‘simple’ as that!