I have a number of patches that show up as missing after a scan. CL5.log is showing error codes 2359302, meaning the patch has already been installed. The patches have been downloaded and copied to the ProPatches\Patches directory but when i try to run the installers they obviously fail with "Already installed".
Also, several batch files in the ProPatches\Install directory going back ~3 months have not ran
Has the target machine been rebooted after patch installation? Many patches will require a reboot to complete the install and may continue to show as missing without it.
Also, make sure your patch definitions are up to date (Check in Help > About), and if you're using a custom scan template, try testing a scan with on of the built-in templates (Security Patch Scan or WUscan) to see if results differ.
If you continue to have trouble I'd suggest opening a case directly with support.