Which version of Sitefinity are you using? This issues has been fixed for 3.0 SP2 release. Actually, here is how the templates mechanism works:
When the provider is initialized, i.e. when the application is started, it checks all the templates in the database against the master pages located in the App_Master folder (without the Dummy.master file). For each master file, if it finds that no template is using it and no template has the name of the master file, it creates a new template in the database with the name of the master page file.
the Telerik team