Software Deployment

I am repackaging an application with InstallShield's Repackager which has a enforced reboot at the end of the installation. When I install on a machine without repackaging it the application will restart properly but when I run the application through Repackager, the installation will complete, Repackager will detect that a reboot is required and when I press the reboot button, it will wait and wait saying that is checking files but will not restart. If I restart manually Repackager does not restart and continue the process.