^Does it look a lot like this? (Bad pic, I know, sorry). If so, it is probrably cynobacteria (red slime algea) and can be controlled in a few ways. The first is to move or aim a powerhead to create an area of high water flow in the areas that it is growing. It does not like water currents and this has helped me out quite a bit since I had that problem.
I have also been told to make sure that you are not over feeding and do everything you can to reduce and keep phosphates down. A lot of flake foods are chalk full of phosphates so you would want to limit how much you feed and when. Lighting is another issue that can promote cynobacteria growth, but that is hard to control in a tank if you have corals or other light sensitive inverts.
My plan was to reduce the amount of time all four bulbs in my light system are on daily as well as to reduce or eliminate flake foods and increase the flow in areas where this stuff was most commonly growing. So far I have been real successful in doing so and havent had a real problem since. I also resorted to a chemical called "Chemi-clean" at the height of my problem and even though I dosed only have what was recommended, the stuff was dead or dying within four hours. I would suggest that as a last resort though. It claims that it is completely safe for fish, inverts, and even benificial bacteria, which I did stand up to its claims in my tank, but like I said, I dosed very lightly and only once because I was leery about taking the risks of losing everything.
