I had this problem when I took apart Winding Mans scenery program for the bits and pieces I wanted and manually installed them..
Check your Assets folder for the; h2od_01.dds, h2od_02.dds, h2od_03.dds etc..Water textures..
these MUST be the same textures that are in your Effects/FXtexture folder..
copy from your assets folder to the Effects/fxtextures folder.. the water textures..(h2od_01.dds, h2od_02.dds, h2od_03.dds etc)
***Back up those in the effects/fxtextures folder just to be safe**
You have two different textures for water(Sea) in your set up and the CFS3 game engine does not know which of them to use..
Or you can reverse the process and copy from the Effects/fxtextures to the assets folder the water textures..
Depending what you want your water(sea) to look like.
One will be lighter then the other will be darker,,
that is why sometimes you get a light looking water texture and then it flashes to a darker water texture and back again to the lighter texture..