Once you record any steps of a Silverlight application, the internal (note: hidden) test property IsSilverlightApp becomes set to true. Once this is set the UI blocks you from unchecking the SilverlightEnabled checkbox shown in the Properties dialog. Even if you clear all steps, and code behind file, you still cannot uncheck this checkbox. Because IsSilverlightApp property is not exposed to the user, there's no way given to turn it back off (short of hacking the .tstest file).

Also note that no error is displayed when you try, nothing even gets logged in the application log. The user is left totally clueless why you cannot uncheck this setting.