Sorry to hear you are having issues. Need to know more.
1) Windows version. Please use Winver.exe for full version numbers.
2) Fences version.
3) And your setting on the "Layout features and snapshots".
I have test out on my system and Fences seem to keep the icons layout/location on my system, after returning from playing a game at lower resolutions. Below is a screenshot of my setting on it.
Stardock Community Assistant.