First of all, I'd like to thank Th3F4114n0n3 for a lot of help in identifying this problem.

It seems as if birch and spruce leaves are shaded using an internal color not affected by the foliage.png file in resource packs. When these colors are used to shade birch/spruce leaf textures that are already colored, the colors are badly affected ingame. Modifiying the foliage colormap does not change the birch or spruce leaves.