Missing Windows Updates in Windows 7 and Windows 2008 R2

Recently, we had a software deployment that required .Net Framework 4.5.2. I deployed the .Net update via SCCM 2012 Software Updates. Within a day, it showed most all systems were now compliant. We were ready to begin testing the deployment of the application upgrade. My colleague came back to me the next day and said the app would not install because 4.5.2 was missing. I began investigating and SCCM still showed it was compliant. We found more and more systems which were missing the .Net. After finally realizing it was not anything that I might have done wrong in the update deployment, I went to a system and manually ran the Windows updates. It was at this point I saw the system was 88 updates behind. The SCCM client had been sending false data back to the SCCM server. I spent much of the evening investigating and finally ran across KB3050265. I downloaded the patch and installed it on my test machine. Low and behold, a bunch of updates appeared in Software Center after running a Software Updates Scan Cycle and a Software Updates Deployment Evaluation Cycle. Had we not been deploying an application that required .Net 4.5.2, we could have gone a long time thinking the updates were deployed. This issue is sporadic, at least in my firm. Some machines were fully patched, while others were not.

NOTE: This was superseded by KB3102810 last November and then by KB313