I'm having a very similar problem with my own map. In fact, practically the same thing; the only difference is that the water surface doesn't render at all and anything completely below it screws up.
I THINK I have all the leaks plugged, but I kept finding new ones last night so I wouldn't be surprised if there were more. But I've been unable to find any thus far. I can think of other things that might be causing issues, though.
I have the water broken up into five segments on my map. The map's theme is an oasis in the middle of an Egypt-themed desert, with two bases on each end. It's my first time mapping so I figured I'd go with a simple CTF map. Anyway...It's broken up into one for the giant displacement hole serving as the oasis, two for the RED and BLU vents that lead into the basement of each fortress, and two for the little exit areas for the teams to jump out of the water.
What's confusing me is, the water surfaces in each exit area don't render either, when they're separate. Is this going to happen due to leaks in the other area or no? I know for a fact that they're perfectly aligned, so it isn't that.
Does the water have to perfectly match its container? If so, it's probably the displacement serving as the oasis screwing it up...
And lastly, since the oasis is comprised of several displacements in order for the vents from the base to work, plugging leaks is often hard, and I just create new displacements and make them look like mounds. This also served to help out the fact that I was finding it difficult to exit the oasis in some areas, so I'd like to keep them, but is plugging the holes up with more displacements going to cause issues?
I'm beginning to think I should just completely do the oasis area over again, but it'd be incredibly tedious :I Oh well. Thanks in advance for any help.