I'm just an online pundit who's barely old enough to legally buy alcohol
Raymond Chen has the answer.
This is a performance optimization.
For a not much longer version, read his post.
If you don't agree with this "design feature" rationale, there is a fix;
"Normally in Windows Vista, the transparency only lasts until you maximize a window. VistaGlazz ensures transparency, even when your windows are maximized."
www.codegazer.com/vistaglazz