So you based your new theme off the default theme right? i.e. you copied app/design/frontend/default/default to app/design/frontend/default/mytheme and skin/frontend/default/default to skin/frontend/default/mytheme ?
Next make sure that you set the theme correctly in admin section, and make sure that it’s not being overridden lower down the hierarchy i.e. make sure that all websites are set to use the default and all stores are set to use the website settings