Prerequisites not installing during msiexec in silent mode

Using InstallShield 2012 Spring SP1 Premier Edition, I have a Basic MSI project that builds a setup.exe. It works great with and without UI (silent mode from admin level command line).

Now I am tasked with having an msi installation file that runs in silent mode – I got it to work with UI, but in silent mode the setup prerequisites do not install. I have read numerous posts on this subject, but am not clear if I am missing something. Is there anything I can do to make the prerequisites install when running msiexec at the admin level command line in silent mode?

(The .msi file I am currently using I got after installing the product using the setup.exe. All works great UNTIL I add the /qn command line option.)
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The logic that controls the prerequisites is included in the Setup.exe if you try to only run the MSI you will lose that functionality
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