Old thread, but just ran across it again and thought that I would respond as there seems to be little to no info regarding the use of this wood, and aquariums, other than this thread. I see other forums are linking to this discussion as well.
Java wood is safe fr aquarium use, but IMO it should be presoaked in a tub etc before adding to ones tank. When presoaking it smells like fresh cut poplar on a beaver dam. Musky. No other way to explain it, it smells, but I've smelled worse. I've soaked larger pieces in the basement, wife hasn't complained so far. Fill tub etc, soak, drain, refill, and repeat until smell is gone, water becomes fairly clear, and wood sinks. Done deal, good to go.
Java wood is a very dense, very heavy wood. Once soaked it sinks like a rock.
HTH