First is that it's typical to get a "thin" slimy film/feel on the sides of the reservoir and tubing after a while. But I'm real confused because you said the blue plastic drum is seen covered with black plastic, but I clearly see the drum exposed in the pictures. That drum is not light proof the way it is in the pictures. Also you said that the water/
nutrients aren't exposed to light because you flood the system at night. But in picture number 3, I clearly see a couple small pools of water. Third the way you have your system setup the nutrients are exposed to all kinds of contaminates, especially being outside in the elements. Anything from soil born pathogens and/or fungi spores blowing in the wind to bugs. There is no doubt that hundreds of bugs are getting in there looking for moisture, and dying in the process. Then you flood the system flushing them through your system.
My first thoughts are that the blue drum is not covered, and thus not "actually light proof" (along with the pools of water in the flooding box) and growing algae. The brown color may be from the coco fiber if it wasn't pre-washed thoroughly (possibly even if it was). I usually let it soak in hot water for hours, then do it again at least 3-5 times before using. The color wont hurt the plants, but I try and leach out as much of the color as I can. The last thought is that you are getting so much organic debris (bugs, leaves, dust and dirt) in the system it's inevitable that you wind up with something growing in it.
That brings me to something else I wanted to ask. You said that you noticed something growing after two weeks, but the system is 4 months old. So how often do you change the
nutrient solution, and clean out the system? In a system design that collects a lot of debris like that, the longer it goes without cleaning it, the more time the system has to build up contaminates, and/or grow bacteria and fungi. I also wonder what the water temp is? Higher temps will aid in unwanted things growing in it as well.