Does a pane of glass cast a shadow?
I suppose it does, but it's very subtle. Hence the fact that there is a penalty of -90 to perception in detecting invisiable creatures/people/items. Of course, one could rule that there is no shadow and other, subtle means of detection are present, e.g., The 'Predator effect' (see the Movies), foot prints, sounds etc. Whichever you choose, the result is the same; a -90 to detect the invisible creature unless of course you are clever and use some other, outside influence.