Domain Problem During ECC Install

I have what I think may be a unique problem in our environment. The Windows domain name and the DNS domain names are not the same. During install the installer selects the Windows domain , i.e. what shows under system name in the computer properties. This is not the DNS domain and as such the .ini files and registery entries get populated with the incorrect domain. Is there a way to prevent this prior to installation, or a way to clean up after? I'm installing on Windows 2008 SP2.