Odd problem here. I have two water shaders, one used for a large portion of the map and a smaller one used for another section. Relatively the same shaders, however, the smaller water shader creates bullet marks on the surface when shot at.
Screenie:

Shader:
textures/duelx_1/water_small
{
qer_editorimage textures/duelx_1/water.tga
q3map_tessSize 2048
q3map_tcGen ivector ( 512 0 0 ) ( 0 512 0 )
surfaceparm nonsolid
surfaceparm trans
surfaceparm water
surfaceparm pointlight
cull none
sort additive
deformVertexes wave 0.1 sin 0.1 0.1 0.1 0.1
{
map textures/duelx_1/water.tga
blendFunc GL_SRC_ALPHA GL_ONE
rgbGen identity
alphaGen vertex
tcMod scroll 0.01 0.025
}
{
map textures/duelx_1/water.tga
blendFunc GL_SRC_ALPHA GL_ONE
rgbGen identity
alphaGen vertex
tcMod scale 1.5 1.5
tcMod scroll -0.0075 -0.03
rgbGen identity
}
}

(Is there anything like that? :???