Please be aware that the value that is defined for the SMSTSRebootDelay task sequence variable is not honored for restarts after the first restart when multiple applications are installed by using a dynamic variable list in Microsoft Configuration Manager. The default restart time-out value is used instead.
A supported hotfix is now available to address this issue. After this hotfix is applied to target clients, the value that is defined for the SMSTSRebootDelay variable will be honored for the whole task sequence. This update applies to Microsoft System Center 2012 R2 Configuration Manager Service Pack 1 and Microsoft System Center 2012 Configuration Manager Service Pack 2 (ConfigMgr 2012 and ConfigMgr 2012 R2).
For all the details including download and installation instructions, please see the following:
3151994 - The SMSTSRebootDelay variable does not work for multiple restarts in System Center 2012 Configuration Manager (https://support.microsoft.com/en-us/kb/3151994)
J.C. Hornbeck, Solution Asset PM
Microsoft Enterprise Cloud Group