I'm curious as to why this continually happens to me also. I am running Windows 8 (64 bit dual screen setup) and often after a reboot Fences does not work. When I run it manually (by launching the Fences 2.11 icon) I get the "Fences does not appear to be loaded. You may need to reinstall". It's very annoying. Any reason why this happens or a fix.
(UPDATE: I noticed that upon right clicking on the desktop to bring up the context menu, after that point Fences begins to work... but not until then.. Bug?)