Microsoft just released a new hotfix KB3079897 for ConfigMgr 2012 R2 SP1 CU1.

"Conditional Access is slow to unblock devices for email access in System Center Configuration Manager"

Symptoms

When you run Microsoft System Center 2012 R2 Configuration Manager Service Pack 1 or System Center 2012 Configuration Manager Service Pack 2 on a server, you may experience the following performance issue or race condition:•Performance issue

After Conditional Access is enabled and deployed, and devices are enrolled and compliant with the compliance policies that are deployed, performance tests reveal up to a 10-minute delay to unblock devices so that they start to receive email messages. The unblocking of devices occurs when compliance messages are received through a fast channel. This processing had dependencies that caused delays. More...

A few days ago Microsoft released another Windows Update that require multiple restarts during the installation.

This time it is KB3075222  which is for Windows 7 SP1 and Windows Server 2008 R2 SP1.

Microsoft has updated their article about these updates here

In SP1 for ConfigMgr 2012 R2 there should be code that can handle multiple restarts during a task sequence but it has turned (as discussed here) out that this is not working on Windows 7.