When I switch from "normal" 3xseparate monitors (with fences on each monitor) to surround mode, all the fences get scaled across the (now) single desktop which means scales across all three screens. If I do nothing and revert to the 3 x separate monitor mode, the fences do return to their correct size and position on the three monitors.
As you explain it, that sounds like Fences is acting as it should. You didn't change the Fences at the surround resolution, so it maintained where it should be when you returned to 3 monitors. But when you changed the Fences in the surround resolution and reverted back to 3 monitors, the fences were then acting accordingly.
What I'm seeing is, you set the Fences for 1 resolution/monitor, but then change it to be 3 different resolutions/monitors expecting it to act like it was set for 3 different resolutions/monitors, but it can't because it's already set for 1 resolution/monitor. The options for preserving the layout on a per-screen-resolution basis works if the resolution stays, but can't if it's changing.
I'm not sure of a solution for you since you do change back and forth between the resolutions. Aside from keeping the 3 monitor layout and then not changing it while in surround, that's all I think you could do.