Using my machine as an example, there were 0 patches missing prior to the new MS patches being released yesterday. After a scan and patch twice over today, 4 patches are now showing as "Missing" per Shavlik even after installing all the new patches. The problem here is that these 4 patches are already installed, and are from 2012 and 2014 that mysteriously now show as missing.
If you try to install them manually, Windows shows that the patches are already installed. If you run an MS Update, it also shows that the patches are installed. I have rebooted 3 times. Why does Shavlik think these patches are missing now?
The patches detected as missing are:
1. MS15-031 - KB3046049
2. MS14-074 - KB3003743
3. MS14-068 - KB3011780
4. MS12-006 - KB2585542