If I remember correctly, the "primary" domain name is the one you signed up for your hosting account with (primarydomain.com). To add other domain names (domain1.com, domain2.co, etc) you have to add them as "addon" domains in your "primary domain" cPanel.
Once you have the main account setup, you cannot change the "primary domain" around anymore as that is now your main (primary) account.
I believe that's probably the issue you were having.
Did I make any sense? heh heh