I'm having similar issues with my Surface Pro 3 (Windows 10 Pro). If I choose the "Store my Fences' positions on a per screen basis," in standalone, Classic icon setting results in minuscule icons that are smaller than the regular desktop icons. When docked using Microsoft Surface Dock and two 1920 X 1080 monitors, all my icons move to the right monitor instead of the left where they used to reside. I have noticed that the option immediately beneath this, "When I plug in a new primary monitor, move my icons to it" is checked by default and grayed out so I cannot deselect it.
If I choose "Preserve my desktop layout by scaling my Fences," then my icons stay on the left monitor, but I get the huge Fences boxes every time I redock after running in standalone mode.
I really wanted to like this program as it does help me organize my desktop icons for my workflow. However, the tradeoff of either having to move all my icons back from one monitor to the other or resize all my Fences boxes every time I dock, is an extra, time-consuming step that defeats the whole purpose. I really hope you can fix this before my trial is up, otherwise I will be uninstalling.