The Hauppauge Win-TV application bundled with their cards allows you to set up a channel # that corresponds to the s-video input => usually Channel 1. I'm not sure if this correlates to the channel assignments in Media Center or not; but I do know the Hauppuage card is "tricky" in this regard --> you have to set up the analog channels FIRST.
I'd try the following: Disconnect the s-video input; then setup the card for the analog input and do a channel scan to set the channels it can receive. Then connect the s-video input and see if channel 1 corresponds to that input. If not, you may need to install and run the Win-TV application first to establish that relationship -- then I'd expect it to work okay in Media Center.
If that doesn't work, let me know -- I'll boot to Media Center and "play" a bit when one of my HTPC's isn't busy recording (they normally run Beyond TV; but I do have a multiple boot setup with MCE available). Also let me know the model # of the Hauppauge card(s).