Can't help you with the particular problem, but I can tell you that Harmony remotes turn them selves off when you press the "off" button to turn off your equipment. Unless you press an "activity" button first, Harmony will not send any signals out.
So, perhaps your particular remotes exhibit similar behavior, where you have to turn on your equipment with the remote in order to make the remote functional.
WMC "power on" signal wakes up XBOX 360 for sure.
6 TV's in the house on FiOS and we only pay $4.99/month to connect them all!!! Power to the CableCard and WMC7!!!