Are updates applied across multiple sites? When running updates for core and modules in a multisite configuration where modules are shared (sites/all/modules), are database updates applied across the multiple site's databases or do you need to run updatedb for each?
You need to run updatedb on each site individually.  Note that as soon as you update the shared code, any site that has not had updatedb run could show errors or otherwise fail to function.  You should therefore take all of the sites offline prior to updating the code, and bring each site back online again after updatedb completes.