Hi, I am trying to replicate a website into a subdirectory using the ReplicMasterSubdir template. I have give the new website an ID of "usa" set the URL as www.domain.com/usa. When I save the website, I get a load of errors telling me that is unable to create symbolic links. No subdirectory is created in the root folder, but database tables are being created. When I try to visit the new site (domain.com/usa) I get a 404 error.

Could this be a problem with the server configuration?

You can verify if the symbolic link functionality when you go in the JMS settings menu.
If NOT, you can use the procedure described in the tutorial video 7

I think that the symbolic link is allowed as you report a message "unable to create symbolic link".
If this is the case, verify that the setting in the website creation has the "create directory" when it does not exists.
I suspect that the "domain.com/usa" directory is not created or can not be created due to a permission error in the "domain.com" that would forbid to create the directory.

If this is a problem of permission, verify the permission of the domain.com and perhaps try using the Joomla FTP Layer to use the FTP to create the directory.

Thanks for your reply, where would I find the option to "create directory when it does not exist?" I can't seem to find it in the website creation options.

If you have the symbolic allowed, this is in the accordeon "Website deploy directory" and this is just below the "Deploy directory" field.
If you don't see the "Deploy directory" field then this mean that the symbolic link is not allowed.

See JMS settings menu and for more info the tutorial video 7 that help you verifying if the symbolic link is allowed.