Idk if it has anything to do with your skimmer but what you're putting in your tank. My skimmate usually comes out a dark green but when I start a fresh batch of GFO or Chemi-pure the skimmate is almost completely black.
You could also be skimming pretty wet. I could be wrong, but skimmers that aren't broken in don't pull as much "bioload" versus one that is broken in, making the skimmate more watery.