Yes, they are all sister companies. Not many people know this and we don't advertise it -- but we don't mean for it to be a secret.
Just to note: name.com and Domainsite have a similar interface (which we tried to make as simple and intuitive as possible), and both of them are giving away Google Apps on domain names now (super inexpensive, really easy to use). It's pretty fun -- worth trying out...
Sorry if you had trouble managing your .name domain at name.com.... Sometimes name servers get quirky with unusual TLDs -- as you probably know, we need to add them to the registry first so that your domain "recognizes" them. On occasion there might be a connection problem between name.com or domainsite.com and the registry, but that's rare... Regardless, if you write support an email they should fix the issue within 24 hours, as the post from last year mentions, we are open to suggestions... Thanks!