Thanks for the reply!
They are using version 11.20.12904.0 of QlikView Desktop. And an older version of the QVPlugin for compatibility. The one that comes with 11.20.12904.0 apparently does not work correctly with their QlikView configuration.
I am using the extracted MSI for 11.20.12904.0 and didn't see two separate installers, just the QlikViewX64.msi. If you do the install manually you can select not to install the QVPlugin but we are distributing to it to a larger audience and would like to deploy this using the MSI without the plugin, unless there is a switch with the executable to NOT install QVPlugin.
I hope that gives you a better idea of our predicament.
Thanks again for your assistance.