I just had the same issue. What I found is that the domain suffix field that you can get to from the console is only for the search domain. In order to permanently change the search domain and actual domain of the host so that it reflects the correct fqdn, you need to make network change from the vsphere client (web or classic). In the classic vsphere client (the one you install) you go to configuration and then DNS and Routing. From there click on properties and put the domain name in both Domain field and "Look for hosts in the following domains". In the web version of vsphere, you can make the change by going to the hosts configure tab, click on TCP/IP configuration under Networking, and the click on the default TCP/IP stack in the pane to the right. From there click on the edit field with a pencil and add the domain name to both Domain, and Search domains. This should resolve your domain DNS issues.
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