If the algae disappears at night and comes back with a vengeance during the day, it sounds like you are dealing with dinoflagellates, not cyano. They can look very similar, but one distinguishing characteristic of dinos is that it forms snotty looking strands, often with air bubbles trapped in the strands or the mat.
If it is dinos, they are very difficult to deal with and a much bigger hassle than cyano!