It must be relative to the lighting--when you don't use pixel shaders, the shade of the entire texture alters slightly in varying light.
Check other (preferably stock) characters in that same area. Do they also do that? It could be that some stray light (such as lights on the other side of a wall) is blocking the view of light on the segments, but not doing so on that entity.
Alternatively, because it's custom, it may be that there's a command in the FPE that handles the "lighting" of those entities.
Evil has a new name. Demo out now!