I have the same issues with Windows 8 and Fences 2.0, whilst all the previous suggestions either don't work or work in a limited fashion. There is a relatively straightforward fudge until support get round to fixing the issue. Just place the icons you want to exclude in a new fence give it a name and then set it to transparent (each fence can have its own settings) and then just exclude the fence from quick hide - works okay for me with drive shortcuts.

Hope it helps someone

Thanks for that information (why I visited the site tonight).  Without 'exclude,' not sure what the point of Fences is.  I have found that version 1 continues to work as well as ever, quirks and all, even with Win 8.  It just takes an extra right click on the desktop after starting up to show the desktop icons (using Win 7 style desktop). 

Works here on 7 ....I shall check it out myself on 8 now that I have all the other SD stuff for 8 loaded...

Just got a new update popup notice for Fences.  The Exclude problem in Win 8 fixed yet?