I run a dual monitor setup also. When i first set it up i tried everything to get it to work with no luck. Finally i gave up for about a week and then had some problems with my comp, so i had to uninstall and reinstall alot of stuff one of these being FS. Once reinstalled it just worked. Not sure that this helped you in any way and I know that Reinstalling is a big pain in the rear, but it seemed to work for me.
Just thought of something else you might try. Go into your display properties and make sure that you have the vid card configured for dual monitors. I had to do that with my new card i just got a few weeks ago to get mine to work with the new card. Hope you figure it out

Hi   can anyone tell me the advantage of a dual monitor system please....or even post a pic of a dual system working so i can see it......3 monitors i think i can understand as sounds like looking out the front and both sides as you fly (but 2) not sure    8)