Apple has posted a revised updater for the OS X 10.6.3 update, which should appear in Software Update on systems for which it applies. It is unclear which systems are needing this update, but apparently not all were properly updated with the original 10.6.3 update. If you are uncertain whether or not you need the update, just run an update check manually on your system and if your system needs it an update will appear.
There is not much information on the differences between this and the previous updater; however, this one fully applies the list of fixes and enhancements for 10.6.3 to the applicable systems. Apple notes that this update is only needed for some systems that were upgraded to 10.6.3 directly from 10.6.0, and not from any previous intermediate version.
The updater is available for both the Client and Server OS, at the following links: