To recreate the problem, just move camera at a position where WAVES can sometimes go above camera level, during the WAVES passing camera height, the skybox becomes the colour of the water (but blank, no pattern)....(using the editor from your distribution, nothing else)
It's due to Hydrax underwater compositor, really it's not a bug, just the compositor design, but I'll change it in the future, don't worry
I suggest you applying this patch(just replace RttManager.cpp and recompile Hydrax): http://modclub.rigsofrods.com/xavi/RttManager.cpp
(I see some reflection artifacts in your scenebuilder screenshot, in the showcase forum).
I used the RttManager.cpp you provided, rebuilt the libraries and dlls, but, still there is something wrong with the reflections, also The Tree in my editor, leaves artifacts on water (Actually the transparent leaves), some of the transparent polygons render as opaque on the water...You can see it in the editor...
Mmm extrange, I'll look into this tonight