Aero is the new hardware-based graphic interface in Windows Vista that includes a ton of eye candy on the new desktop. Aero stands for Authentic, Energetic, Reflective, And Open. It is intended to be cleaner and more powerful for the user.
When you do a clean install of Windows Vista its possible that your video card will not be detected correctly causing Windows Vista to default to "Windows Vista Basic" in the Appearance Settings. If your unable to see the background of your desktop through the borders of open windows then more then likely this has been set by default. Once you install your video card drivers you can follow this article to enable Aero.
Right click anywhere there is open space on your desktop and left click on Personalize
Click on Window Color and Appearance
Click on Apply and then click OK
When you get back to your desktop you should be able to see the background through the borders of open windows now!