Why cant I fully patch my SQL and Exchange Clusters with Configuration Manager ?

Well the case is that Configuration Manager doesnt support patches that require User input and isnt therefor replicated to the Configuration Manager environment. So theese updates need to be deployed in another way, although many customers patch clusters manually so it is not a problem for them, but you wont see the compliance status for thoose patches either. So Config Mgr admins out there keep an eye on this´so you wont miss important patches for your environment.

To find updates that cant be installed with Configuration Manager you can query your SUSDB for patches that require User Input.

USE SUSDB
SELECT SecuirtyBulletin, DefaultTitle, KnowledgebaseArticle, InstallationCanRequestUserInput
FROM PUBLIC_VIEWS.vUpdate Where InstallationCanRequestUserInput = 1

Source of material: http://social.technet.microsoft.com/Forums/en-US/configmgrsum/thread/a4ea7e76-0589-4eb4-a31f-a17b6ab9ea41