Cynobacteris can grow in all conditions and can even grow in the healthiest of tanks. Usually occuring in low flow and areas of lower light. The Chemi-Pure pad has been know to help. I have also had luck with some stuff called Red Slime Remover. It comes in a littl bottle and is a powder. It contains antibiotics and can cause some die off of your nitrifying bacteria alond with the Cyno.
If I were you, I would invrease flow to the infected ares, siphon out as much as possible and keep up with your water changes. I have seen Cyno in tanks considered Labrotory grade and in tanks as crappy as mine. It knows no natraul enemy such as snails or crabs but, I have noticed Mexican Turbos occasional in the stuff..
Good luck with your problem...