InstallShieldTuner and MST issue

I am running tests to do a silent install. In my tests, I am using the Standard All Client install.

I am using IntallShieldTuner v6 to create the mst.

I am using a batch file to run the msi in conjunction with the mst.

When this is working I will use SunRunAs to run as an administrator.

At the moment, I am not using the /qn ,flag to make it run silently, so I can see what effects the mst has on the install process. I actually ran the batch file with the /qn flag on originally, but it uninstalled verything…read on.

When changing mst properties with the InstallShieldTuner, under “Organization\ Features”, regardless of what I flag as “The Feature is installed on the local drive”, when you run the batch file, and the install process begins, all components I have flagged as “…install…” are flagged as “…will not install…”.

Am I missing something fundamentally simple?

Any comments or suggestions would be gladly received.