I've had issues on a number of occasions where if I create a new Folder in a fence and give it a name, and suddenly a number of other existing folders are also renamed with the same name. So now I have to search through my fences to make sure it hasn't happened when creating a new folder.
Also, when I select and deleted un-fenced files form my desktop, sometimes other files and folders are randomly deleted from within fences (even though they were definitely not selected for deletion)
I'm really liking my organized desktop but am getting paranoid about creating and deleting files. Are these known bugs that are being worked on?