It's interesting reading all your guys' posts... in my case, I got the same error message complaining about emulation... I had A-120 (newest), CloneCD (188.8.131.52), and D-Tools installed. I checked and double checked and had NO emulation options enabled on any of the programs. Still, FarCry would not start up, I kept getting the error message and was getting pretty pissed.
I uninstalled D-Tools (the first and only thing I did) and then the error message went away.
So who knows... but I am really getting sick of these types of error messages... especially when I shell out $45 or more on average per game.