After logging in on a Windows 8 or 8.1 system and removing Windows "Metro" or Store Apps you notice Shavlik Protect detecting missing updates for the Windows Apps (such as MSWU-1006 or MSWU-1007).
Windows Metro/Store Apps are installed along with the OS. If you are still seeing updates listed missing when scanning with Protect it's because the Apps have only been removed for a certain user or users on the system, but the apps technically still exist on the system.
If you want to exclude these updates from coming up within scans, you can do so using the steps in this document:
We're not currently aware of a definite way to completely remove Windows Store Apps, however, it may be possible to completely disable Windows Store Apps via additional configuration. The following documentation from Microsoft provides more information about the Windows Store and Apps:
Shavlik Protect 9.x