I fixed some problems with skies and water. For the skies, I removed the Jedi Academy level (the one from The Jedi Academy (
http://www.thejediacademy.net)). For the water, that's caused by the Matrix Reloaded map.
If you don't have those, look for .pk3s that have either has the shaders skies, bespin, and doomgiver or look for the same names, but under the textures folder.