Hello,
Sorry to hear you are having issues. From my experience, this might probably due to OneDrive Desktop Sync get turn on after your last Windows update. It have been reported before by others with same symptom you mentioned above. What you did by manually re-layout your icons into Fences should stick. Just make sure to save backup/layout snapshot after your have done it.
Thank you.
Basj,
Stardock Community Assistant.