I have the same problem after the update. I rebooted several times. No change. Then I opened Fences and on the Home page unchecked "Enable Fences" under basic options. Then I rebooted. Then I opened Fences. It asked if I wanted to enable Fences. I clicked no. After everything was up, I opened Fences and checked the "Enable Fences" check box. This fixed it for me until I moved an icon on the desktop which moved when I enabled fences. Then the problem returned after several screen redraws. So it works until you move an icon.
So, when you reenable Fences it seems to return to a memorized icon placement. Then when you move the icons back, Fences flashes the screen a few times and then disables itself.