One thing I have noticed is that if you change a feature on the index template, you have to save and reopen the template for the changes to take effect in the other page templates.
Example: Removing the 'Sidebar Menu' from your index template, if you go to another page template it is still there and the option to remove it is grayed out. Once I saved and reopened the template it then recognized I did not have a sidebar menu in the index and removed it.