We are seeking some input from the other modders that mod the source code of FPSC like us (Flatlander, Scene Commander, TZK, etc).
Cathy and I still work in v1.17 and have three developments that are half way completed in this version, so upgrading is
not an option at this time. In our source version, we have ported water and it works great. There is one issue we have been trying to solve that has us totally stumped, which involves water and skyboxes. Warning- there are quite a few images posted to demonstrate our issue.
Creating a test level, we add our water which is turned on via trigger when the player hits it at the start of the level. I am noticing that the skybox looks like it is "bleeding through" an enclosed level. I have some screenshots to demonstrate what I mean.
These first two show the level with water. The line in the "setuplevel.fpi" that defines the skybox is commented out (in other words, no skybox). The water looks perfect for us.
Now I switch the line in the "setuplevel.fpi" to use a skybox. It is a desert skybox 9brown sand, blue sky). When you are looking at the water, you will see the "brownish" color of the skybox appear along the water edge.
Now we change the skybox to use a "black" skybox. It is not fully black, but RGB 5/5/5. You can see the "black" along the edges in a few spots.
In the above examples, it appears that the level that uses water in an enclosed area will need to ensure no skybox is used for the enclosed level to keep any "skybox bleeding" into the water.
Here is another enclosed level for our Egyptian game. I used the "black" skybox for this test. As I look across the water, it looks normal. If I look upward slightly, I see a black distortion", and returning normal it disappears.
But, if I comment out the skybox in that same level, the water never shows that "distortion".
I have checked our water code and it is in line with the current source (r725). I am stumped at the skybox/water/enclosed levels. Why does not using a skybox appear to be the best for enclosed levels? Does the media being used (such as segment walls for the sub level, cave wall entities in the other level) have anything to do with this?
We've come to the conclusion that commenting the skyboxes out for the enclosed levels only that use water is the best approach for us at least in the version we use. This issue is not affecting our ability to complete the development, but is one of those things that we keep coming back to at our age saying "oh yeah, we need to solve this issue and not leave it". We would appreciate any insight to this.

There's no problem that can't be solved without applying a little scripting.