Took awhile to figure this one out. Apparently setup.exe just passes it's command line parameters to msiexec.exe. To set up unattended, I used this command line:
setup.exe /QN REBOOT=ReallySuppress
This avoids the weird errors when just launching the MSI package for installation. Keep in mind though that you likely need to reboot the system for the software to work. You might however try scripting the launching of this:
It's placed into a key called "dla" under HKLM\Software\Microsoft\Windows\CurrentVersion\Run.