I find it strange that anything on the application side would mess it up. More likely drivers are deliberately screwing performance in doom3 with multi-monitors, to make ppl run in single monitor mode, because that way theres more VRAM available, and therefore more likely to win benchmarks..
But thats just me being cynical for a change.
P.S. ITs the 13th today, and my copy of Doom3 just dropped through the post!