I've had the same problem. I used zimbra.my-domain.com to test it out, then couldn't create my-domain.com. After deleing zimbra.my-domain.com, I used the command line tool zmprov to try to create the domain. Here is the result:
[zimbra@zimbra ~]$ zmprov cd my-domain.com
ERROR: account.DOMAIN_EXISTS (domain already exists: my-domain.com)
[zimbra@zimbra ~]$ zmprov gad
So you can see that my-domain.com does not show as existing, but somehow it thinks it does.
Meh, my dummy domain was filtered out of the original post by the forum software. Dont put words between the angle brackets.