I found a SkyBox from another Game and changed it, to fit into Minecraft. But the colors from the Skybox as a picture is not the same, as the Skybox ingame (see Attachments). The ingame Map is a Void, just if your wondering why there is nothing. Its just to see the full sky and not just the upper parts.
You need to change the sky colormap as well. The skybox uses colors from the colormap. Assuming you're using MCPatcher features, you can make a folder in the mcpatcher folder called "colormap" and create a sky colormap called "sky0". The mapping is exactly the same as grass and foliage colormaps. I imagine if you make the colormap completely white, it might use the original colors from the skybox you added. Not sure about that though.