Hello there!
When a deployment is going to be executed a Run Mode must always be selected. A Run Mode defines under which account the scheduled task will be run on the client machine. There are currently 3 Run Modes for packages: System Account, Scanning Credentials, and Currently Logged On.
When executing a deployment package with the Currently Logged On or with Scanning Credentials Run Mode, the installer/command/... will use the active desktop session to display its information, hence the presence of the command prompt.
If you want the deployment to be fully silent, the deployment would have to be run under the System Account Run Mode. The system account is the only Run Mode that will allow a package to be fully silent. Only with this Run Mode will there be no command prompt window displayed on the monitor when a deployment is executed.
