Your first stop when troubleshooting Group Policy-related problems should be the client computer's Application Event Log, followed-up by the Resultant Set of Policy tool.
The Windows Installer will automatically run in a limited user interface (read: silent) mode when invoked from Group Policy-- there's nothing you have to do to the MSI files. (If the MSI author was malicious or stupid, though, they might be calling Custom Actions that present UI even when running in a limited UI mode, but that's not likely...)
I suspect that you have one of the following going on:
Your clients have defaulted to asynchronous policy processing which is notorious for making GPO-based software installation unreliable and non-deterministic. See Group Policy installation failed error 1274 for some details.
Your clients can't access the path where the MSI file is located (either because of permissions, name resolution, or inaccessibility because of network topology / configuration). The client's Application Event Log will tell you that.
The GPO isn't actually applying to the clients. The RSoP tool will tell you that.
The MSI is set to a language other than the client's OS-default language and the tick-box in the software assignment's properites hasn't been set to cause the clients to ignore the language. (Apple iTunes and QuickTime have this problem.)
Likely the client's Application Event Log is going to tell you what the problem is.