This can be caused by numerous things, however, the most common issue has to do with the settings in the .htaccess file.
To view that file, follow these steps:
1. FTP into your account to the /home/username/public_html directory (username is your actual username).
2. Open up the .htaccess file and try to *cut* the contents leaving it blank. Save the file and quit.
3. Go back to that site and it now should show as www.domain.com, which is correct.
If this does not work, please contact our Support Team.