I'm quite late to the game here (just got my Flirc) but what I have a similar situation for which I've come up with a workaround.
I have a Vizio smart TV with a Vizio QWERTY remote, which I am using for both Flirc and the TV. When I switch to the TV's Netflix app for example, I don't want the keys I use in Netflix to register with the Flirc/XBMC. I also want to keep my PC running (so no sleep/wake solutions).
Originally I wanted to find a way to detect (for example with EventGhost) when my HDMI was switched from my HTPC to another source. That didn't work for me. The next best thing for m