Is it like that for only custom maps? I used to have a problem with the sky because it started to go like all crazy and stuff but then I just re-installed and it fixed it. Have you tried re-installing?
If all else fails, type r_fastsky in the console. If it says 1 then type r_fastsky 0 to fix the problem. If it is already 0, then this isn't the problem.
f_fastsky 1 can cause the sky to be black, that is why I mentioned this.
ok, well the r_fastsky is currently set on 0 so that is not it. Changing the texture quality from 16 to 32 didnt do it either. And I have reinstalled the game and has not fixed much at all.