this the same as what I am experiencing, posted in the fences 3 beta thread.
I have a problem with fences 2.90. After windows has loaded, the desktop and taskbar will be displayed, except for the fences and folder portals, and no icon is displayed. I have to right-click the mouse in order for the fences to appear. The "Configure Fences" entry in the context menu will appear after the right-click.
This is my setup:
Windows TH2 10.0.10586
Fences 2.90
Deskscapes 8.50
This happened after upgrading my motherboard to an asus maximus hero 8.
Thanks!