Hello,
What patch scan template are you using when scanning? If you are using a custom template can you try one of the built in templates to see if the same issue occurs (Security Patch scan or WUscan).
Is it possible to list which patches continue to show as missing?
Also, verify that you have up-to-date patch definitions. You can check this in Help > About > Version Info. The version for Defintions, patch assessment and patch deployment should match what is listed at this site:
http://protectessentials.shavlik.com/
Help > Refresh Files should update the definitions if it appears that they are out of date.