When my friend gave me his old computer when he got a new one, the water started doing this. I assumed it was cause i had to use older graphics drivers cause the newest ones weren't working and certain problems with some programs had to use a driver somewhat older than the one immmediately previous to the latest.
I've just lived with it, it's kind of annoying and distracting sometimes, but, whatever.
Unclicking shiny water doesn't help it any.