Sounds like you accidently changed the default scene.  From the noob to pro wikibook:

Quote - You can change the default scene (and return to a personalized one when pressing Ctrl-X). Just modify the scene and arrange dialogs to suit your needs, then click File > Save Default Settings. Your current scene will now be used as the default when you click File > New. This is very handy indeed. To return to factory defaults, you can delete the file which contains those settings: .B.blend in your home directory. Starting from version 2.44, a new Load Factory Settings item is available from the File menu.