Hey spik. First and foremost, the darker nights patch doesn't change the water's surface color. It's the original water that reacts so poorly to darker light settings. I never got around to adding this to the patch because, well I sorta forgot.
As for your issue, I believe you're using the wrong ID. The water values in the Sky & Fog settings are fake. Either way you're not counting properly. Should have been a range from 3835-3850 (only 16 rows). Anyway, the real water color is the next column over, the one named Water Settings on the dev wiki. So take 215*18-17, and you get 3853.
Your range in LightIntBand.dbc is therefore 3853-3868. Rows 3867 and 3868 are going to be the settings you're looking for, if my memory serves. Take the original values in column 19 and scale them to a darker color. I used this:
http://www.w3schools.com/tags/ref_colormixer.asp when making the original patch, it works great