When I first installed SH4 and put in the 1.3 patch I played many missions before I put in any mods. I noticed this same effect you describe at night. It appeared to be god rays/light rays in the night sky when I was on the deck looking around. It only appeared to be outside, no problems with inside shots. It had my attention a little, but the game was new to me and had no idea if that was normal.
I slowly installed ROW mods one at a time to see what they did and how they changed the game. I eventually got to the whole thing. I can't recall if I still saw them or not after ROW mod. I took all my mods out to install path 1.4 then threw in the ROW mods and the light rays at night are gone. What the hell I did that made them go away is beyond me and yes my light rays box is checked. I'm a big fan of the graphics of this game so I monitor what I have graphics set at. Perhaps the post-filter processing? (think that what it's called) Not sure what this would do to the night sky or if it has an affect at all on this situation.
If you narrow the problem down, let us know. Like I said, I had them once and I noticed it exactly like you did. Now I don't have it. I didn't adjust any graphics card settings with NVIDIA software. I think I installed the ROW mods in the order the creator posted in his thread, where as I did it recklessly before
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Take care