I can't remove directX dependancy from the game, all transparency effects in the game rely on it...
Do you have this water problem with Amy only? It seems really odd...
The water has no textures...it's a custom DirectX effect that draws the deformed background on the water box.
I'm sorry, but at the moment I have no idea what can cause that problem on your end.
EDIT: I'm working on a compatibility option to use a simpler water effect. That may solve your issue once 1.08 will release.