The elite does do the passthrough. I have one of the current models with a Mac feeding it HDMI. Works just fine. I can't speak to the SC=71 but passthrough is usually passthrough. NO clue about Windows Media Center.
Windows HDMI problems often are the result of using obsolete (buggy) HDMI graphics and audio device drivers.
The first thing to try is to download and install the most recent drivers provided on the Web site of the manufacturer of your graphics hardware.
That said, turning something off in the HDMI chain frequently causes problems for Windows. Recovery usually involves forcing a reset of the HDMI device drivers. In the past I've used AVR Audio Guard's "Reinitialize Device" option to do that, but I haven't needed to do a reset for a while. My computer has Nvidia hardware and I keep its drivers up to date. I suspect they've fixed some bugs recently which used to require resets.