Well, after many times logging in to try to replicate it, only to find out that it wasn't happening anymore, I found out what REALLY causes it. The water texture "disappears" because of the time of day and the angle that light hits it. When it's night time, or early morning, there is no light hitting the water. Without the light hitting the water, you just see right down through it, without seeing the greenish color and the water rings around things poking up through the water.

It all seems like I was just having perfect timing with logging in while it was dark, and repeated instances convinced me the graphics weren't working. Funny how when I'd changed the Environmental Animation to Normal, I started logging in during the day when the water is visible....