Honestly, I think it's an unadvertised rite of passage for most reef tanks to go through a cycle like this in their first few months or so... This tank is about that, isn't it? If so ... continue on, as you are doing, and it should clear itself eventually. It's when the tank does have measureable nasties like nitrates and phosphates that you can't account for when you start to have REAL headaches. For example, my ritteri tank, just can't keep nitrates under 30.
I can't keep any corals in that kind of sewage. Where do they come from? I have no idea, it's not like I overfeed, it's not like I don't have a good skimmer. I guess it's just having a 24" anemone turns out to be a bioload beyond my wildest imagination. But weirdly I dont' really have any filamentous algaes in the main tank except for in the overflow strainers. I guess the urchins, rabbit and abalone are basically keeping things clean that way. But I do get the occasional bad bout of cyano, man I wish I could figure out a way to deal with this nitrate problem (tank is about 1.5 years old now).