Much of this was stated above.
The reason Cyano forms in low flow areas is from waste settling on the substrate and breaking down. I also feel that it is more related to Phosphates than nitrates. The reason carbon dosing can lead to cyano is that it creates a dominant strain of bacteria that does not use the Phos as much. Cyano has photo type properties meaning that it grows More during the day and lessens with out light. This I believe is also helped during an extended period of darkness by allowing other forms of bacteria, that do not need light, to multiply. I think you should increase flow to the areas that have the cyano, vacuum as much as possible, do not use flake food, run some sort of Phosban or GFO and then darkness.