I'll be watching this with interest too.
I really like MEP, but stopped using it because I had the same problem.
In stormy or overcast weather my water was a very vibrant blue, not the grey I can see in these screenshots (very nice pics by the way
)
I'm wondering if maybe it only happens with some types of GFX card.
What type of card do you have fitzcarraldo?
Mine is an ATI.