Does any body how the game decides what colors are invisible. For Example "World/Shared/A000_piping.bmp" has a dark yellow color that is invisible in game, but "World/Shared/A000_rails2.bmp" uses a light gray for this. All the textures don't have an alpha channel and they use different colors (even different color indices).
Unfortunately, I haven't been able to figure out how LRR determines which colours are supposed to be transparent. The closest thing I've been able to do is create transparent particle effects which works by treating pure black (000,000,000) as fully transparent, pure white (255,255,255) as fully opaque, and everything else inbetween partially transparent. Then, in the Surface Editor in Lightwave Modeler, you have to go to the Advanced tab and set Additive Transparency to 100%.