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Is the Windows Update service enabled on the target system(s)? This service needs to be enabled - it can be set to manual or automatic, but if it's disabled there will be many updates that will fail to run installation.
In Protect if you go to Tools > Options > Scheduling do you have it set to use the Shavlik scheduler or Microsoft scheduler?
On the target system if you go to C:\Windows\Propatches\Install check the newest files for either a .bat or .his file - which do you see? A .bat means the scheduler has either not run the .bat file yet or the installation is not complete. A .his means the .bat was run successfully and renamed to .his at the end of deployment process.
You could also try manually running one of the patches in the C:\Windows\Propatches\Patches folder to see if there is a specific error during install.
I hope that helps.