There are two other methods to change Primary DNS Suffix.

1. Using Regedit
   The primary DNS suffix is stored in the registry in the following location:
    
   HKLM\SYSTEM\CurrentControlSet\Services\Tcpip\Paramaters
    
   You might want to change the values for the following registry keys:
    
   1. Domain (REG_SZ)
   2. SearchList (REG_SZ)
       
       
2. Using Group Policy
   Since you don't want to join your servers to a domain you can't use Group Policies with an Active Directory source, but you will still be able to change the Local Policies with ease, although it won't be pretty security-wise
    

1. Log on to a Windows Vista or Windows Server 2008 box with an Administrator account with the exact same password as the Administrator account on the Server Core box
2. Run gpedit.msc
3. Open the Computer Policy
4. (Open Policies)
5. Open Administrative Templates
6. Open Network
7. Open DNS Client
8. Double click the "Primary DNS Suffix" policy
9. Enable the "Primary DNS Suffix" policy and type your suffix
10. Press OK
11. Open the "DNS Suffix Search Order" policy
12. Enable the "DNS Suffix Search Order" and type your suffixes
13. Press OK
14. Log on the Server Core box
15. Perform the following command:
     
    gpupdate
     
    The settings from your Local Policy should take effect.
     

You might want to consider running ipconfig /registerdns after changing the Primary DNS Suffix.