Microsoft has just updated the following KB Article:
A command-line action that has a linked package doesn’t start in System Center 2012 Configuration Manager
Symptoms:
A task sequence (TS) doesn’t start as expected in System Center 2012 Configuration Manager. This issue occurs if the Run Command Line Action sequence step has a link to a package, and the deployment for the task sequence has the Download all contents locally before starting task sequence configuration applied to it.
This problem occurs only if multiple task sequences include the same package, and the package has a larger source size.
Full details at:
http://support.microsoft.com/kb/2961924