I'm late to this thread, but I hope this helps some one.
To fix 3 monitor issue you must install the Quadro/GeForce drivers (
http://www.nvidia.com/object/macosx-304.00.05f02-driver.html). However, you must first set your system definition to MacPro 3,1 in multibeast to install drivers. (At least that is the case with Gigabyte GA-Z68X-UD3H-B3 (f12), MacPro 4,1 and 5,1 will not boot with this MB and the drivers will not install with MacMini or iMac.)
My process:
1. Clean install from unibeast
2. Installed Kepler 6XX Graphics Drivers via multibeast and set SD to MacPro3,1
3. Install Drivers from Nvidia link above
4. Reboot
5. 4 Displays detected (3 monitors (1920x1200 ea) + movie projector)
I hope this helps someone!