Isn't the Green rupee supposed to Make the boxes at the scientists house full so i can jump on them o_o ?

PS: awesome game
5:30:59 game time x3 4337 zombie killzzzz

In order for the green boxes to appear, you need to put the rupee into a specific device. it looks almost like a rectangle with a dull green light on it, narrow at the bottom. (the one in that specific room is pretty hard to find though)