Are you testing this with one SharePoint server or multiple? If it is multiple and you have apps on different servers, it will create the SS Service on the box with the application using it.
If that is the case, there is a bug in the commandlet, not AutoSpInstaller, that you will have to stop the other instances of SS so it can set the key on this box.
If that is the case, there is a bug in the commandlet, not AutoSpInstaller, that you will have to stop the other instances of SS so it can set the key on this box.