Maybe it's just my eyes, but I don't see any difference with the color on the pads when selecting from a specific color family to assign to the Atom pads.
For instance, I would like to use a dark yellow for cymbals and a light yellow for hi hats. When I choose two different yellows—one dark, one light—from the yellow family, I don't see any difference on the pads themselves, they both are the same yellow, although they're clearly distinguishable in the color selector. I'm in a dark, dungeon-like room fyi. 
Other than this, for me, the Atom rocks!
Thanks Presonus!
