Not sure if you figured this out but I came across this post while having the same problem, and found a solution I wanted to share.
1. Add Flirc to your Harmony remote through the MyHarmony desktop software. Enter "Flirc" for the device manufacturer and "XBMC" for the model number. This will import a preset configuration of Flirc controls.
2. Rename the "Power Off" control on the Harmony to "Power Toggle" (this will make sense in a minute).
3. Install the Flirc software on your HTPC. Make sure you select the Streacom/SE edition where you can map the power button.