@ FireFly: I’ve tried changing the parameters but even with all white the spots were there.
@ Shaderman: Its the same result with or without the light compile.
There is another thread in here where someone is having the same problem, however it is on the hud models (the arm and weapons). I have noticed similar things when playing.
I made another test. This time with the texture saved as .jpg - however I got the same result.
This is the actual jpg I used:

It looked like this ingame:

This is its shader:
textures/chruker/mountain_battery/metal1_grey_010
{
qer_editorimage textures/chruker/mountain_battery/metal1_grey_010.tga
surfaceparm metalsteps
{
// map textures/chruker/mountain_battery/metal1_grey_010.tga
map textures/chruker/mountain_battery/metal1_troublemaker.tga
rgbGen identity
}
{
map $lightmap
rgbGen identity
blendfunc GL_DST_COLOR GL_ZERO
}
}
And this is the sky shader:
textures/chruker/mountain_battery/sky
{
qer_editorimage textures/skies_sd/siwa_mask.tga
nocompress
q3map_lightimage textures/skies_sd/battery_clouds.tga
q3map_sunExt 0.75 0.70 0.6 160 -60 30 3 16 // <red> <green> <blue> <intensity> <degrees> <elevation> <deviance> <samples>
q3map_sun 0.75 0.70 0.6 1 -60 30 // Dummy - Used by the sunshader command
q3map_skylight 100 4 // <amount> <iterations>
sunshader textures/chruker/mountain_battery/sky_sun
surfaceparm noimpact
surfaceparm nolightmap
surfaceparm nodlight
surfaceparm sky
skyparms textures/skies_sd/wurzburg_env/sky 512 -
{
fog off
clampmap textures/skies_sd/siwa_mask.tga
tcMod scale 0.956 0.956
tcMod transform 1 0 0 1 -1 -1
rgbGen identityLighting
}
}
textures/chruker/mountain_battery/sky_sun
{
qer_editorimage textures/skies_sd/siwa_mask.tga
nocompress
cull none
q3map_nofog
{
map textures/skies_sd/siwasun.tga
blendFunc blend
rgbGen identityLighting
}
}
I’ve tried with the q3map_sun and q3map_sunExt set to 1 1 1. I’ve tried disabling the skyparms and q3map_lightimage lines. No matter what the spots and miscoloration was still there.