Hi,
I am not certain what is causing that problem for you, but it's probably something to do with the way you're logging in.
Are you logging in as 'root' or as a user? That is, when your FTP or shell access program asks for a username & password, are you entering 'root' for the username, or something like 'yourdomain'?
Usually if you're getting errors when trying to CHMOD, it means you're trying to alter a file whose ownership is not assigned to the username you've logged in as. If you can log in as root that should solve the problem. If you do not have root access, contact your host and tell them what you need to do, they should be able to log in for you.
Thanks for using Draupnir!