The only thing that that has changed in this respect is that the masked off area is still visible in the preview, but doesn't render. So it works as it should, only not in the preview window, probably because that's multithreaded now. In TG2 you could see what you're doing, which I admit is better. They'll bring that feature back, no doubt, it's known at the alpha forum. But the dark gray ending up as black is still the same as it was, I always whiten the water masks before entering them into the opacity tab, unless they're really black-white already.