Only worry about the color if it clashes with the walls :-P
Color can indicate the following:
age of comb
age of brood
type of pollen
type of honey
more brood raised in it
Older capped brood is darker than younger capped brood.
Are the queen cells inhabited by larvae yet? If not, then it isn't necessarily a problem yet.
Also, if the queen cells are on the face of the comb (Are these new packages?) that would indicate a probable supercedure instead of swarm. Often new packages will supercede the queen for whatever reason. If this is the case then there isn't a problem with destroying the queen cells, they may eventually accept the current queen.
Welcome to the crazy confusing world of honeybees.