I think I have been hacked. Why do I think this? The website functions just fine. However, when I login as the administrator, I can not make changes to the any portion of the theme. As a matter of fact under "Appearances" it has two "Background" selections rather than "Theme Options" and "Background". I have deleted and reloaded WordPress, the Theme and all plugins.
So is it in an MySQL table or a PHP file or both?