Glitch with GHII and MCE on XBOX 360
I found a weird glitch with my XBOX 360 when I was trying to use it as a Media Center Extender. Turns out if you have the Guitar Hero II guitar plugged into your XBOX 360 while trying to use Media Center, you will not be able to control Media Center via a remote control.

It took me a few days (and several disconnects, reconnects of my MCE box in the XBOX 360 Dashboard) to figure this out; however, as soon as I unplugged the guitar, my Harmony 880 (and my XBOX remote) both kicked back in.

So if you're having problems with using a remote with Media Center through your XBOX 360, try unplugging your guitar.