Looks like that same thing that happens when the screen "breaks" at the start of battles and at the end. Even that Looper/Weapons texture that appears at the bottom.
(Never bothered getting there with Dolphin with how the sound is but from the Picture it looks exactly like it.)
The screen breaking effect is properly emulated for me, at least. Other than that underwater effect fail, the only other graphical bug I've encountered is visiting the save menu from an airship. Well, and the shadows, of course.
^ Screen Break with that Warping effect.
(From 3:29 here
http://www.youtube.com/watch?v=djYuy1fYVm0 )
Unless it was fixed in newer builds, but it's still interesting to see that they might be related, since those Weapons and Looper background Textures show up on both.
I'm without my desktop to take a screenshot at the moment, but the effect is indeed emulated properly now.
Well just saying incase the problem is related. (In both Looper Textures show up)