We managed to find out the reason for this bug.
This shows up when you turn on anti-aliasing on DX9.
This happens not only for me, for many.
Distribution Direct X is from your package with the engine.
Screenshots below:
DX9 64bit
No anti-aliasing
Render.SeaEffect = true;
DX9 64bit
Anti-aliasing - Level4
Render.SeaEffect = true;