Ever since I upgraded from Windows 8 to Windows 8.1 I have experienced this problem.
In Windows 8 everything worked great, but after I upgraded to 8.1 only one of my three monitors was detected. At some point I figured out that if I turned off crossfire then all three of them would be detected after I rebooted. But I would like to keep crossfire enabled if possible.
I have two Radeon 5870 GPUs crossfired, all of the monitors are connected to one GPU. Running the latest drivers 13.12