I installed f.lux V3.12 and it worked only on a single monitor. When I installed it I was running on only a single screen via remote desktop (RDP). When I came to work and used the PC physically in the same room only one screen was affected by f.lux. I re-installed f.lux over the existing version and by doing this I found that both screens were then affected as expected.
I have not tried rebooting the machine yet as it's possible this might affect behaviour. If it reverts to working on only a single monitor I will repost to this forum.