OK… so when it comes time to upgrade mediawiki, and you happen to have more than one mediawiki site enabled on your website, you have to do some trickery in order to get the database to update properly.
In my case, I have a script that matches against the $callingURL in the LocalSettings.php file. If it matches a specific case, it changes the site name and database name to a different one so that a different set of data is presented. Not that big a deal really, until it comes time to update the database due to a new version of mediawiki.
When that happens, and you run the upgrade.php script as they state, it will only upgrade the default database, and not the other one, because the $callingURL won’t match. In this case you have to temporarily modify your LocalSettings.php file so that it forces the other database, and then it will upgrade that other database without issue.