I have a domain registered with GoDaddy. But, a free email account supplied with this domain doesn't work. Perhaps, it is because I relocated my Wordpress blog from GoDaddy's hosting to another company.
It could be, if you changed the nameservers on the domain. These tell which DNS to use, which contain the settings on how email should be handled. If you are using a 3rd party nameservers the DNS here is not active. You can check in the Email Setup Center:
Under "General Information" ideally it would say:
Domain settings (DNS):Valid