Ok, that explains some
About water:
There is a limitation/bug or whatever in HL2/source that prevents you from making expensive ("see through water") in multiple heights on the same level, if you do, it will ALWAYS be buggy and wierd, also it will NOT help making one cheap and one expensive one.., you need to use all cheap water OR change the layout so its all on one level,(no waterfall ) if not if will turn black randomly etc.