I'm having the same issue using the free version of fences on Windows 7 Pro 64-bit. It seems to have started following a reboot after applying some Windows updates today. Also, immediately after that same reboot, the computer's Display setting had changed from 100% to 125%. (Right-click on desktop > Personalize > See also: Display) I've never had that happen after applying Windows updates, i.e. the Display setting has never gotten changed from 100%, which is the default. But even after setting the Display setting back to 100% and playing with the size of my desktop icons, the problem with Fences persists.
Bottom-line description of the problem: I can no longer create a vertical fence that is wide enough (and tall enough) for just one column of icons and have all of the icons wrap to just that single column. The most they will go is two columns, and when you make the fence narrower than that, the second column of icons gets hidden, even though the fence is plenty tall enough for the icons in the second column to wrap over to the visible area of the first column.
From the very beginning, I have always had single-column vertical fences on my desktop, and this has never been a problem until today.