@Iszh,
After some quick testing, it appears that using certain combinations for the water LERP settings can cause that effect. I also found out that one can actually make some truly hideous looking water if one puts some effort into it.
Anyway, the fix for the map generator is simply to further restrict the possible values for those settings. If time permits, I'd really like to remove the random element from the water. Using a set of pre-built oceans themes (from which the map generator could choose one), would probably result in a more consistently appealing result.