well.. i will blame your video card. i had a problem like yours when i installed 71.89 NVIDIA driver for my card (maybe unproperly installed?) . i was in the water temple and it was completely dark, like if there wasn't light ( a completely dark place, i only could see things with lights from torches). i repared this mistake reinstalling my old video card drivers. it happens only in deku forest? there isn't any other place where gets black, or "non-illuminated"?