Hello,
Sorry to hear you are having issues. Not really sure what you mean by auto-arrange? Did you set the sort to none within the Fences?
Also, do know that Fences 3 not compatible with Windows 11. It best to move on to Fences 6. Also, do know that you can do 30 days free trial on Fences 6 and see if the issue still appear with it.
Thank you,
Basj,
Stardock Community Assistant.