Your examples (for TextApp.app) show as being built for 10.6 / x86_64.
When I start up and create the new project TextApp it defaults to 10.5 and i386.
Also, the MainMenu.xib is MainMenu.nib for me - and when I go into Interface builder there are additional differences (such as it does not say TextApp in my menu interface but instead NewApplication).
I have completely uninstalled the Dev tools and reinstalled from the Snow Leopard DVD and still get the same defaults. I have not been able to figure out how to set the default OS and Arch for new applications.
Could you please explain how to get Xcode set to the proper defaults that you are using in your examples?