I have a similar issue but it may not be exactly the same. My icons appear on the wrong monitor, but fences are on the correct monitor. Fences 4 does not restore the snapshot as what's shown in the snapshot thumbnail, it gets confused on where the icons-without-fences should go. I'm on Windows 10.
This started happening after I upgraded to Fences 4 from 3. Fences 3 never had any issue with this. This is important, because this is behavior is new with Fences 4 - at least in my case.
A reboot fixes this issue, but I don't want to boot up my computer and then reboot again for Fences to work.
This is likely because I turn on the monitors after I start the computer - and monitors may get enumerated differently. But Fences 3 never got confused about this. This seems to be a bug in Fences 4.
I also have a slightly unconventional display setup: Display 1 is disabled (no output), while Display 2 and Display 3 are my regular monitors. I don't use any multi-monitor apps or utilities. Just a disabled display in nVidia Control Panel.
Fences 4 doesn't seem to keep up with changing enumeration. But of course, the problem can be deeper than that.
This started happening immediately after I upgraded to Fences 4. No other changes were introduced to my system (no driver updates, no changes to monitors or displays, nothing else was installed or uninstalled).
Hope this helps somehow, but this seems to be a long running issue. I'll try to downgrade to Fences 3 for the time being if I can find the installer.