Although this comes as an InstallShield installer, it by default will try to install Direct X 9.0c and Speech Engine 5.
If you use the standard setup -r, these two programs don't get included, and your silent setup will fail.
To get around it, do the following..
Run setup normally.
Opt to install the main app and SpeechEngine.
At the EULA for SpeechEngine, browse to your temp folder, and you should see the extracted installer for SpeechEngine (SpeechVoices.msi) - copy the whole folder somewhere.
Exit the installer.
Now run setup -r, and ONLY select to install the main application. You should now have a setup.iss to allow you to install the main app silently.
After this, your batch file should include the setup for DX9, if required (see this site for copious notes on installing that silently), followed by a standard msiexec /i /qn for SpeechVoices.msi, and then your setup.exe -s for the main program.
If you wish to save the mission files in the default location, you'll need to change the permissions for C:\Program Files\Immersive Education\Mission Maker\My Missions using subinacl, or similar.