I've been having this problem with certain shaders that I want to be non solid, translucent, cull disabled, light from shader/entity sources are being chopped up and resulting in shadow blotches in the lightmap.
I did an insane amount of testing and recompiling to try and solve this, but it either resulted in the texture blocking light or the blotches. I give the shader light parameter's it only faces one direction, I take away certain surface parms, it screws with its function in the map. I tried moving the entity light away or inside, or below, same results.
If someone could suggest an alternative method to fix such a problem that would be great.
I'm not entirely sure what's causing the splotches, but here are a few pointers. One of them might be the source of the problem.
surfaceparm noimpact probably doesn't do what you think it does. If you shoot a rocket at the beam, it will just disappear rather than just go through the beam.
Remove surfaceparm lightfilter. If it's a beam of light, it shouldn't be casting coloured shadows and could be the reason for the splotches.
sort additive: any reason why you have to specify this? Sort is generally handled automatically, so unless you actually have a sorting issue, you shouldn't need this.
I got this when a light entity was dead level with a textured face. It'd be considered as a light that was casting on the surfaces around it for some of the light traces, and discarded for some of the others. The end result was a random set of splotched 'on and off' light traces just like your 2 shots.
For me, shifting the light entity manually away from the surface by a few units fixed the issue, but it looks like I could have edited the texture and got the right result.