I've set the 'Welcome User Email' under 'New Site Settings' to the following:
Dear USERNAME: Welcome to the SITE_NAME portal which provides information on our policies, processes, >procedures, templates and forms. You can also view the SITE_NAME news, calendar and >contacts.
Here is your login information: Username:USERNAME Password: PASSWORD
Click here to log in - LOGINLINK
The problem is that when the user receives the email, the "SITE_NAME" parameter is the 'network name' for the wordpress install, not the name of the actual blog they have just registered to.
This code https://gist.github.com/1331582 overcomes the issue for the user confirmation email that initially gets sent out when a user is added, but I need it to apply to the 'Welcome User Email'.