The most common error is editing the files under the wrong user.
Navigate to manage domains in the panel, find the domain you attempting to edit and look in the WEB HOSTING column. It should say “fully hosted - User: NAME” The files under that user are the files apache will serve to a web browser. To make a change you MUST log in to that user.
See also: http://wiki.dreamhost.com/One_User_Per_Domain_Policy for a more complete explanation of how users work.