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One of most important and critically used feature in configuration manager 2012 is Software updates .
It is always challenging and import task for any sccm administrator to achieve good patch compliance success rate within the given SLA(Service level agreement).
When you enable software update agent setting in client agent settings,a policy will be created with this setting and stored in SQL Database.
So when client initiate machine policy,it communicate with management point which includes the software update client feature installation instructions to be installed or applied on the client.
In this process, Client will create local GPO with WSUS Settings by leaving automatic updates .
If you do not disable automatic updates (Via GPO) leaving the door open for the WUA to do things on its own outside the control of Config Mgr including installing any updates approved directly in WSUS (including new versions of the agent itself which are automatically approved) and rebooting systems which have a pending reboot.
Neither of these is desirable in a Config Mgr managed environment and thus the recommendation for disabling automatic updates.