Emulator

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Have you searched the issue tracker for a similar issue?
Yes, but it's closed, and has reappeared in recent builds.

Game Name?
The Legend of Zelda: The Wind Waker

Game ID? GZLE01 (NTSC-US)

What went wrong?
When moving the camera around, the ocean waves and shadows flicker.

What did you expect to happen? No flickering

What steps will reproduce the problem?
Climb the ladder to the lookout tower on Outset Island and look down towards the bridge with the rupees, and you'll see the waves flickering while the camera moves.

What version of Dolphin were you using?
3.5-555 and various newer builds since then, including the latest 3.5-1178, all builds since 555 should be affected

64 or 32 bit Dolphin?
x64

What version of Dolphin used to work?
3.5-548

What Operating System were you using and what are your hardware
specifications?
CPU: i7 3930k 3.2ghz
RAM: 16GB DDR3
GPU: Nvidia GTX 670 with 314.22 drivers
OS: Microsoft Windows 7 x64 SP1

64 or 32 bit Operating system?
64 bit

Any other relevant information or links to logs:
Memory card save: http://www.mediafire.com/download.php?nn9icmmbjdc5g3x
Fifi Log(10 frames, 2 don't seem to capture it): http://www.mediafire.com/download.php?d9zp8erh9c3r2sp
Save State: http://www.mediafire.com/download.php?rgd9vz70adcbs47

Settings:
Dual Core ON
Idle Skipping ON
JIT Recompiler
Cheats OFF
DSP LLE
DSP LLE on thread OFF

Video Settings:
1x native
Anti-Aliasing: None
AF: 1x
Post Processing: OFF
Scaled EFB Copy ON
Skip EFB from CPU OFF
EFB Copies -> Texture
Texture Cache: Set furthest to right by Fast
External FB: Disabled