Skimmate color is going to depend on how dilute it is. Lighter skimmate, like you have, is removing more water. Darker skimmate is just more concentrated. You can adjust the water level in most skimmers to get more dilute or more concentrated skimmate.
In general, you're probably removing more dissolved organic compounds when you are getting lighter skimmate. If it's darker, more of the waste is likely dropping back into solution before it is removed from the tank water. The upshot is that you have to be more diligent about monitoring your salinity with a light colored skim, as you are removing more saltwater on a daily basis. Replacing just for evaporation will result in decreasing salinity over time...