in screenshot 2 and 3 with the rocks, have you tried info_lighting them to something nearby, but outside the light? Doesn't base lighting on the object come from the origin?
Also, I had this issue w/ cp_frozen in stage 2. I just recently switched from the coldfront skybox to the Viaduct one and it no-longer has that issue. I noticed that there was a micro-seam along where the lighting was, so that might be it.
Also, Also, I think Ezekel had an issue with this during canyon fodder, might want to ask him because I believe he resolved it.
If a solution to remove these don't pop up, you could always "cover them up" with other random light sources, lanterns for example.