There's only one pump in the tank plus the return, but it's a Maxspect gyre. Placed high up it hits the opposite wall in a sheet, travels down that wall and then across the sand. It's a great pump to reduce dead spots. Flow is important, but won't solve the issue at all once it gets started. Mine became a major issue (with hair algae up to 3" long that covered over half the tank. I got rid of it by attacking it. Every three days or so I'd take a form bristle brush (a couple different sizes) and scrub the rocks. Once I had as much off as I could I'd siphon as much as I could get out. The Cyano I sucked out more often anytime I'd see it beginning to mat. Once I had about three fourths of it out manually I felt safe in treating it chemically as well as still scrubbing manually. I didn't want to treat chemically till most was gone because I didn't want to see a big die-off that could pollute the tank. I then started treating it with Vibrant and also went out and grabbed a couple of urchins, a Sea Hare and a lawnmower blenny. All worked their little asses off, but I think the Tuxedo Urchins were the key because when they hit a patch they left nothing behind except scraped rock.
The key though is you have to scraped the rock with brushes (hard) and in some cases take out corals and brush it off them as well. Once you get about 80-90% out natural processes can finally get a head of it.