I run two monitors from two seperate graphics cards, don't have much of a problem, though I did not expect some of the slow downs that it produces (running the same game in two windows (different views)) I expected the cards to run at optimum without drawing anymore of my resources.
The only issue I have really come across though is when running a video on one monitor if I move it to the other it loses all of it's colour set up and basically becomes a mess. Other than that no problem.