Ive checked the logs when compiling and it says there is some leaks, but when i goto find them the things it says are leaking arent.
Im at a loss ..


The thing that it says is leaking is just an entity near the leak. In hammer main menu, Map>Load Pointfile, will create a red line. The line will start at the entity, and will make its way around your map until it leaves your level through the leak.
Fix the leak and your water will look like water again.
I've also found that oddly vertex-manipulated brushes won't seal the map either even as world brushes. It doesn't matter if they're not concave, or even if they seal directly on the line of a normal brush; the engine refuses to recognize them as world brushes, or at least that is my experience with them, may not be a problem for others.
Also, another thing to check: Sometimes this causes a problem and sometimes it doesn't, but check to see if the outlining walls go into one another, that is, do they line up on each other's edges, or do they clip beyond the edges? Make sure that they line up exactly on the grid and on each other.

This room your mentioning, is it completely separate from the main map and 3d skybox (different from the regular skybox), and its own walls are what separate its interior from the void?
Just to clarify, your skybox texture should not be encompassing the entire map like a box circumscribed about the map. It should be used to just cover areas where there are no other walls or other visual disturbances to block the "void" from sight (check the Valve sdk maps).
Another clarification: The 3d skybox should be a box that encompasses everything that is not in the map, that is, it would be completely separate from the main map, and yes, look as if it was a hollowed out box completely covered in the _skybox texture. You use it to display big outdoor scenes that are built at 1/16 their original scale, and the sky_camera entity blows them up 16x that size to make it seem regular; it saves on resources and allows Source to render huge environments beyond the player's access at decent frame rates.
Your room however will not be in either of these. It should sit out there in the void all by its lonesome with its own walls (that are not covered in _skybox material). Regular brush-based walls not covered in the _skybox texture are also adequate to blocking the void. The skybox just adds a sky texture, so yea, you probably wouldn't see it used at all in a total indoor map with no windows.


