Are you using the correct scan tool?
In Manageability, one of our top issues and areas of customer pain in the SMS space is around the incorrect scan tool being used with software updates. This is a big call generator and our highest area of critical situations (CritSits) with Premier customers. The issue manifests itself with patches not being detected and/or patches not being installed.
One way to keep yourself informed on which scan tool to use can be found in the monthly Detection and Deployment Guidance articles. You can always find the link to the current month's article in the monthly Security Bulletin Summaries (current month is always here ... http://www.microsoft.com/technet/security/default.mspx). The link to the Deployment Guidance article is under the DEPLOYMENT section of the bulletin.
You can also see the full list of monthly detection and deployment guidance articles here ... http://support.microsoft.com/kb/910723
In each article, there is a table which summarizes detection and deployment guidance for each security patch.