There seems to have been an unannounced update in the detection logic for MS12-006
I had a similar conversation with another customer late yesterday where MS12-006 shows missing when it was already installed. It was determined there is a detection logic issue with MS12-006 and other patches that supersede it. A file detection issue with the file cng.sys which is updated by all the patched in the supersedence group.
Apologies for the issue, we will have a fix for this in the today's XML release.