I have four XBMC setups going through the same TV!
Primarily testing different units for family and friends, my main HTPC runs OpenElec, then I have a mini pc running Windows 8.1 that boots with XBMC launcher, a TLBB and an AppleTV2. I recently purchased a Harmony Ultimate to help control these units plus had three Flirc devices in storage which I upgraded to v2.4 firmware. Initially I had setup all three Flircs using the Flirc/XBMC device profile on the MyHarmony app, which worked flawlessly on three of the four units (the MyHarmony AppleTV profile works great btw).
However I noticed the Flircs were indeed getting confused as I was sending key presses for one unit, the other two would respond - not ideal. I must add that I keep these units on at all times to receive automatic subscription updates so turning them off when not in use is not really an option.
As suggested in the above post, I changed the profile for my windows pc to the Microsoft/MCE Keyboard profile which worked well. However the TLBB did not respond at all when I used the Matricom/G-Box Midnight profile so I'm back to using the Flirc/XBMC again (just too lazy right now to manually do it with the Flirc utility).
I do have a wild idea for the Flirc guys though. Would it be possible to pair (or bind) a Flirc to a unit's mac address? I imagine you would enter it via your Flirc utility app and then click to pair. Purely optional of course for those wanting to use two or more Flircs through one TV. Just a thought.