I'm not quite understanding why you have a need to launch shutdown.exe from within the package.
If the package requires a system restart, the Windows Update Agent will initiate that system restart (provided the return codes for Restart Required are properly defined).
If the package does not require a restart, then no restart is required.
If you want to do a system restart after package deployment, the place to do that is with the Patch Manager Update Management tools, select the option "Always Reboot"
