Your vision is like from a camera, at a point you can both above water and below. But there is a point in your character's head that tells the game to put a dark overlay if it is in the water. Your first screenshot shows that the point is not underwater but your vision is.
I can confirm that this bug exists from 1.4.5 to 1.4.6 pre-release. Also it happens regardless of what gamemode the player is on.
It's just the order of the generation code that's need to be rearranged. I don't know much about it, but if the structures that generate first get overwritten by the next structures generated, the portal code should be the last built. If it's the other way around (as in blocks cannot overwrite another), portal goes first.