It's possible that you are setting permissions for the wrong user. This has happened to me in the past, I was setting permissions for "MY_USER_NAME" when I should have been setting the permissions for "www-data" user.
The following links may be helpful to you:
http://superuser.com/questions/144984/setting-permissions-for-specific-user-and-groups-in-linux
http://www.perlfect.com/articles/chmod.shtml
http://www.linux.org/threads/file-permissions-chmod.4094/