If you are having trouble getting XBMC to read the IR commands from your remote from within Windows, I would highly recommend trying IR Server Suite which required little to no setup and got my XBMC setup reading IR signals from my MCE remote in no time.

The remote control (IR system) I purchased was the following:

AVS Gear HA-IR01SV Infrared Certified MCE VISTA Remote Control

I noticed that the traffic coming from search results for 'IR Server' were starting to increase on my other blog post about 'Cheap HTPC with XBMC and IR', so I figured I would add a few more details to this post.