"fillmode" is FFP parameter wich allows you to render just the vertices or edges of an object. You can find the lines at the end of the Water.fx file in the render passes.
Its sometimes really usefull for debugging...
I solved it by replacing the line 716
Fillmode=(fill_mode_var);
with
Fillmode=3;
that way I could see some awesome water shader
What I didn't like about it is that looking up from underwater looks a little weird...
