Fences doesn't align its icons to your desktop's grid.  In order to place the fence anywhere you want, it needs to have its own grid separate from the desktop's.  I've only used the free version, and only on Windows XP Professional, but it uses the same icon size and spacing settings that my desktop uses.  (Not sure what the difference is in the way Fences behaves on the two systems, or even if there is any.)

In the picture you provided, it doesn't look like Fences is using the same icon spacing that your desktop is using, which I find a bit odd.   Maybe you found a bug in Fences that only happens in Windows 7?

As a test, make eight new folders on your desktop.  Arrange four of them in a square inside a fence, and arrange the others in the same way on your desktop.  If you can't tell whether or not the spacing is different, take a screenshot and post it here so I can try to help you figure it out.