They showed up whenever I did a beta build of the game before its release, but when the final release came out, they were just black. I decided today to just redownload and overwrite my data20060614.pk3 and see if it was just a fluke, but they still don't work. Is it a known problem?

Yes and i can also tell you the fix..
Some custom maps share a shader file with Nexuiz 2.0.. well almost the same, the one in Nexuiz 2.0 is much larger. So far i only noticed this error with:
space-fun.pk3 stralenex7_beta1.pk3 stralenex8beta2.pk3 stralenex9.pk3 stralenex_ctf__beta1.pk3
All maps except space-fun are now part of Nexuiz so you can either delete them or rename the files to .pk3_ so that they are not loaded and mess up the sky. divVerent created a fixed version of space-fun by just removing the shader file from the pk3 file. You can find it here: http://hector.rbi.informatik.uni-frankf ... nofficial/

Thanks, I deleted stralnex7_beta and stralnex9 and the skymaps worked perfectly