I had the same problem and just within the last two weeks seem to be getting over it. It was very frustrating because I use RO/DI water, I don't overfeed, (I barely feed at all and everything seems fine: 1 clown, 2 damsels, 1 pseudochromis, and a coral banded shrimp and various snails, crabs)
I had green hair algae, some slimy stuff on the sand, and some sort of brown leafy algae growing over the rocks. I was picking clumps off the rocks all the time. Now, all of the sudden, the growth of this seems to be receding. The only things that I have changed is that I switched from a Red Sea Prism skimmer to a aqua C Remora and also, I aimed my power heads a little bit differently so that the surface of the water is broken more and is more turbulent.
Assuming for the moment that either one of these factors has anything to do with the change, my thought was that perhaps I was having a problem with carbon dioxide trapped in the water because of lack of oxygenation and not having enough turbulence to provide enough "clean" surface area on the top of the water.
Another thought I had was that since the aqua C pump is supposed to push about 400 gallons per hour, maybe the increased flow of water is the reason. The first thing I noticed is that the rocks below the skimmer seemed to clear up and the purple coralline was much brighter.
In any event, the stuff on the sand is gone and while there are a few places where the hair and leafy brown algae are still present, they no longer seem to be expanding and appear to be diminishing.
Bottom line: I think the jury is still out on my situation, but the preliminary lesson seems to be more flow and better oxygenation result in less algae.