How to incorporate msiexec parameters in a mst

You're seeing the dreaded scourge of asynchronous policy processing. It's not a "feature" (and was default-off in Windows 2000 but default-on in Windows XP and above) and causes exactly what you're seeing-- non-deterministic behaviour with processing some types of GPO settings.

In a GPO that applies to that computer, add the following setting:

• Computer Settings
  • Administrative Templates
    • System
      • Logon
        • Always wait for the network at computer startup and logon - Enabled

After you set that (and allow the GPO to replicate if you're in a multi-DC environment), do a "gpupdate /force /boot" on the subject PC. It will reboot and you should see the software installation occur.

The "Always wait for the network at computer startup and logon" slightly slows down the startup and logon because all GPO extensions are allowed to process, but the upside is that all GPO extensions are allowed to process.

Have a look at what Scott Willeke's Less Msiérables (LessMSI) can do for you ...

http://lessmsi.activescott.com/

Use it to extract and change guids and/or contents of MSI, repackage and execute your 'install twice' need.