I have the exact same problem, and it is rather annoying. It works fine if you use Large Icons, but if you're like me, they're too clunky.
Right click your desktop, choose Personalize > Windows Color > Advanced Appearance Settings. From here you can do one of two things, either change the icon font to a smaller size or increase the vertical spacing of the icons
This does not work for all icons, only
If anyone can solve this mystery, I and many others would be extremely appreciative. Funny how such a little thing can be so annoying? :P