When you clone a server you need to Sysprep the machine. To sysprep Windows 2003 server (This is needed to reset the GUID), Put the Windows 2003 server CD in the server and Goto Support -> tools -> Copy Deploy.cab file to the server desktop.
Now open the cab file and extract the contents to a system file (in the desktop for example)
Here you can find sysprep.exe file. Run the file and set the shutdown mode to Reboot. You may need to choose ‘factory’.