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.
4. Click the power button on the Flirc software, and hit the Power Toggle button on the Harmony remote to record the command. FYI this will shut down your computer after doing it but Flirc will have learned the command before shutdown.
Now the Power Toggle button can be used to both turn on and shut down your machine, and it won't have any crossover with other Activity buttons!