Hi rldev, Fleat
I'm also using a Harmony remote (the 650), and I'm using WMC primarily as a PVR/Live TV and XBMC for most other HTPC activities.
I'm having some issues with the responsiveness to button presses, particularly direction buttons.
For example, sometimes there will be no response to a direction button press, and then maybe the third time I press it there will be scrolling in that direction of the menu, but past the point I wanted to get to.
Did you have any such issues with your setup?
I'm using Windows 7 and the Flirc XBMC "device" for my remote.