I have a triple monitor setup and have had this problem for a while. Fences simply sucks at handling multimonitor systems, custom icon spacing, and hidpi scaling.
BUT, the good news is that there is a workaround. After installing the Nvidia driver update, reboot immediately. I think Stardock is using some wonky display enumeration (along with dimensions, offsets, icons spacing, and hidpi scaling), and rebooting before a snapshot is taken will allow fences to enumerate however it's used to doing it.
Now if I could just drag and select any icons in the left column of a fence without overshooting by half the screen, that would be nice...