We have been deploying QV Server v11 SR1 as part of our installation suite using a command-line installation (not extracting the MSI, but passing parameters to the setup.exe). In order to address a couple of issues, we need to upgrade to SR2. Is there a way to do the command-line install w/out getting the "Do you wish to upgrade the server?" prompt?
The .msi installation packages in QlikView Server are wrapped in .exe's (that's the ones you download). The .msi packages have all the functionality you need to do instrumental and silent installs for your needs. Look up Orca (msi viewer tool) for insight into the .msi's and look in your temp folders for the .msi's that gets extracted when you run the .exe installers for QVS.
If you cannot find the .msi's, contact QlikView Support for instructions on how to extract them.