In one of my recent attempt to configure SCCM 2012 SP1 for windows 2012 R2 updates, I saw that the clients was scanning the system for updates but they were not getting installed on system.

Upon checking UpdatesDeployment.log on target system, the message “Waiting for third party orchestrator to initiate installation”

Once again going through the client settings and its description provided at http://technet.microsoft.com/en-us/library/gg682067.aspx#BKMK_ComputerAgentDeviceSettings helped to figure out problem.

In client setting “Additional software manages the deployment of applications and software updates“ need to be set to “No” which was “yes” in this case. Once the changed client settings is downloaded on system the update installation will start.

Check WUAHandler.log for status.