Microsoft released the following KB article on 16th October which includes a Hotfix:
Dynamic applications do not install in System Center 2012 Configuration Manager Service Pack 2
Symptoms:
Some applications do not install when you try to install them by using a dynamic variable list in a task sequence. This problem occurs when one of the applications restarts. Any additional applications that are involved in the same step do not install after the computer restarts. There are no specific errors recorded in the logs. Instead, the task sequence continues to the next step.
Full details: