I have a Euro-Reef skimmer, and mine does the same thing every now and again. Depending on how much material there is to skim, you may get some thick stuff, and other times you get thin BRIGHT green stuff. Just cleared out a cup of it yesterday.
If it was dark at some point, then your skimmer is still perfectly fine... just needs to be slightly adjusted so not as much waste gets dumped into the cup. I adjust mine every other day, just to make sure everything is fine. In most cases, this is not needed, depending on your skimmer... but I'm anal about those kind of things and spend about 2 hours each day just fiddling with my tank.