The download includes a colour.properties file which allows biome shading to be applied to blocks. Unfortunately it doesn't work on Mod added ores.
I had this problem with Misa's texture pack and my textures.
http://forum.feed-the-beast.com/threads/64x-misa-compatibility-textures.3719/
Check out my topic, I've got instructions of how to "fix" this. Basically to turn off the biome shading on normal stone.
Here's the extract from that topic
Also, edit color.properties from Misa's texture pack and put a # in front of palette.block./misc/stonecolor.png line. This will eliminate stone being shaded to biomes, and stop ores not being shaded. Better fix then not using color.properties at all.