Could you let me know how I can contact you directly? I'd be happy to try to help you resolve the problem.
The Vault server installation, while it, too, utilizes MSDE (using a different instance name), also utilizes IIS (or its own built-in web server). The Inventor installation of MSDE, when it's installed, does not require IIS. Therefore, some of the checks done by the Vault server installation process are not relevant to the Inventor installation, which also utilizes several of the same checks, just not in as obvious a manner.
You can reach me directly at jeff.pek@autodesk.com.
Thank you!
Jeff