I get something similar. My main monitor's taskbar disappears. Rebooting fixes it for a while. I also use Display Fusion, but am considering removing both Start10 and Display Fusion, and switching over to Classic Shell for my Start menu. I will keep using Fences.
I get exactly the same delayed start problem with the latest Fences 2.13 on Windows 8.1 on a Surface Pro 3. I run Fences fine on my Windows 7 computer, and I had hoped to use it on this laptop, but as soon as I installed Fences 2.13 it hangs the Windows desktop for about one minute. Soon as I disable Fences and restart Windows my desktop displays right away. I had never installed Fences on this laptop. It is a completely fresh install of Fences. I do run Start8 on this laptop