Also most curious, the PDF included in that zip file renders with symbols visible through the water. Or is it because they are on top of the water?
Attached screenshot taken from Adobe Acrobat Reader 9.5 on a Windows 7 computer.
Footleg The area symbols are all on top of the water, except for the one labelled '0 sand' (but is actually clay - oops) The numbers relate to the order the areas and their boundaries were drawn, the higher the numbers were drawn last and render on top of the lower numbers. The screenshot you sent makes '8 bedrock' to '10 moonmilk' opaque, but with Foxit Reader 3.3.1 they are translucent. If you compile the dataset that I posted on the wiki you will find that each of the symbol sets gives different behaviour in this respect. It depends how the individual symbols are metapost-ed. Bruce