Hello,
Sorry to hear you are having issues. First, do know that Fences 3 is not fully compatible with current Windows 11. Would like to advice to upgrade to Fences 5 for better compatibility with current Windows version.
As for the icon arrangement, please try, disable auto arrange icons in Windows desktop context menu setting and on each Fences set to sort to none. And try different setting on your Fences auto-layout adjustment setting.
Thank you.
Basj,
Stardock Community Assistant.