On March 24th, we revised the SQL Server 2005 Service Pack 3 Microsoft Update logic to offer when a clustered instance is detected. When the logic was originally released, the logic would not offer if an instance was detected to be clustered.
Since the SQL Server 2005 Service Pack still requires credentials to launch the process on the PASSIVE node, the update needs to run in attended or user interface mode. You should scan the ACTIVE node first and then the PASSIVE node for applicability of the service pack . When the update runs on the ACTIVE node it is expected to patch the ACTIVE node and PASSIVE instances. We recommend scanning the PASSIVE node for applicability of the service pack to ensure all component have been update to the service pack.