Have you taken any additional steps since your first post?
If so, what steps?
The Remotes made for XP MCE are not compatible with Vista or W7 and also are no longer made. Microsoft does not make the remotes anymore either. If you have a MS Remote it will not work with Vista or MCE.
This is not a new issue.
Microsoft MCE Remote problems with Vista MCE - The Green Button
techPowerUp! Forums - View Single Post - Human_error's guide to USB IR receivers and media centre remotes
Microsoft Media Center IR Remote And Receiver at TigerDirect.com
As you have not provided any specifications of your hardware I can only provide basic replies.
I also am certain that if you properly remove the IR Receiver and drivers that WMC will not prompt for a remote (assuming your TV Tuner is compatible).