Installing Office via the “Custom Installation Wizard” is common practice in this kind of environment and I was surprised not to have seen this issue or a fix for it documented anywhere out on the web. Perhaps my Google search skills need sharpening, however, after many tests and tweaks I found my fix. Re-installing Office 2003 without re-installing the 2003 Resource Kit caused my issue. Not only does Office and all of its keys need to be deleted, but the same approach needs to happen for the 2003 Resource Kit as well. I deleted all instances in the registry of:
SOFTWARE\Microsoft\Office
SOFTWARE\Microsoft\OfficeCustomizeWizard
Then, after everything is uninstalled and cleaned out, re-install the Resource Kit and create a new transform .MST file with the specifications for your exchange environment.