I used to get Jelly looking water occasionally in the standard game. It got worse with 1.3 and worse again with this mod, initially. I got rid of vertical sync and it went away. (Disabled in the .ini file as well as the options screen)
Not sure if it will work for anyone else, but it sorted it for me. Only downside is I get some tearing on the inside sub screens but I can live with that.
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