Broken window regulators. There are a number of threads but I don't know the search term for finding them. Essentially, when you open the doors, the regulators are just taking up a small bit of slack in the cables and the windows themselves don't drop enough to really notice. When you unlatch the top, the all slack gets taken up and then the windows drop more.
PS: Try this to get started:
http://986forum.com/forums/general-discussions/25704-window-regulator-permanent-fix-stretched-cable.html