I think the default supported install of ZPanel is with a subdomain. Are you sure you answered the install questions according to the recommendations?
From ZPanel website:
4) Enter the FQDN of the server
! VERY IMPORTANT ! FQDN stands for Fully Qualified Domain Name.
It is the domain name you will use to access your control panel after installation.
It MUST be a subdomain of the root domain you have. it must NOT be the root domain that you will use for a public website. Example:
Some valid FQDN for zpanel : zpanel.mydomain.com
Read more at http://docs.zpanelcp.com/?node=51