Today Microsoft released a new KB targeting problems with the Install Software Updates hanging when you use the Install Software Updates step in a Task Sequence. This issue has been around since Configuration Manager 2007 and is still an issue in Configuration Manager 2012 with some updates.
“Software Updates That Require Multiple Reboots may Cause Task Sequence Failure within Configuration Manager“
The KB article is applicable both to Configuration Manager 2007 and 2012. Keep an eye on the KB above as it will be updated with more updates as they are reported, that will save a lot of troubleshooting time!
“If a Configuration Manager Task Sequence that leverages the Install Software Updates step installs a software update that triggers multiple reboots, the task sequence can fail to complete successfully.”
The first reboot initiated by the software update is properly controlled by the Task Sequence. However the second reboot request is initiated by a Windows component (typically Component-Based Servicing) and therefore not controlled by the Task Sequence.
“To resolve this issue, it is recommended that any updates that require dual reboots be applied using the normal Software Updates feature of Configuration Manager instead of Task Sequences. The following software updates have been reported as requiring multiple reboots. This KB will be updated as more updates are reported.”
For more information http://support.microsoft.com/kb/2894518/