Look at the properties of the MSI. Do you have a button that is similar to 'Unblock'? If so, unblock it.
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That'll be Windows UAC (User Access Control) blocking you, in short, I would suspect . That wonderful "nice on paper, horrible in reality" security feature...
As long as you're running the install as "Local System" you shouldn't get to see the UAC screen.
Also, you don't need to have a batch with all the answers - you can call the MSI directly and feed it command line parameters in the command line parameters section as an alternative. A crude screenshot of what I'm talking about is included below:
... so your TRANSFORMS-file (at a guess) should be easily enough called through there .