I had similar problems to them I solved with those lines, I thought it was just my install..
in vietnamsea_data
[WaterTextureMaterial]
DepthBufferCheck=TRUE
DepthBufferWrite=FALSE
RenderedInOrder=TRUE
AlphaTestEnabled=TRUE
CullMode=CLOCKWISE
LightEnabled=TRUE
SpecularEnabled=TRUE
EmissiveEnabled=FALSE
FogEnabled=TRUE
AmbientColor=1.000000,1.000000,1.000000,1.000000
DiffuseColor=1.000000,1.000000,1.000000,1.000000
SpecularColor=0.500000,0.500000,0.500000,1.000000
SpecularPower=50.000000
Reflectivity=30.00000
ZBufferOffset=4.000000
BlendOp=BLEND_SRC_ALPHA
NumTextureStages=2
TextureStage[01].TextureName=
TextureStage[01].MipMap=TRUE
TextureStage[01].FilterEnabled=TRUE
TextureStage[01].StageColorOp=TEXTURE_MODULATE_DIFFUSE
TextureStage[01].StageAlphaOp=TEXTURE
TextureStage[02].TextureName=
TextureStage[02].MipMap=TRUE
TextureStage[02].FilterEnabled=TRUE
TextureStage[02].ReflectionMapping=TRUE
TextureStage[02].StageColorOp=TEXTURE_BLEND_TEXTURE_ALPHA
TextureStage[02].StageAlphaOp=DIFFUSE
Water on medium in my case. For some reason the water effect shader cause problems, maybe just in the medium water setting I have to use..
Also it happened to me that two sea textures, I suppose from deuces, but I may be wrong, were interfering, Vietnams1 and vietnams2.tga.(their size one meg) They can be removed and the terrain will use the default ones in the .cat file.