If the mod you're playing has custom biomes, it ought to have its own colourmap. Either it will have a brand new one, or it will map on to the existing one.
Your problem comes down to one of two things:
The mod itself is misbehaving. Take it up with the mod maker.
The resource pack only colours the pixels that matter for Vanilla. The colourmap appears as a smooth gradient, but it need not be. Since the vast majority of the colourmap is unused, some pack makers may not bother with a smooth gradient, and only put dots and splotches in key spaces. If the mod maps to the existing map, and the existing map is 95% white, or black, or anything else, that's the colour that will show in game. If this is the case, add a green-or-whatever gradient to the white pixels. If this doesn't fix the issue, refer back to point 1.