Cyano is really weird. I've had the stuff growing on the damn powerhead output and also skimmer output! Flow doesn't necessiarly kill it, however, I think settled detritis can promote it, so increasing flow is probably worthwhile especially if you have deadspots.
If you're having bad probs I'd suggest making sure the source water (after ro, etc) is clean. I had a problem with contamination after filtering - so like every topoff and water change I did, I was adding fuel to the fire. Maybe it's a no brainer, but I never really considered this as a potential risk before.
As far as where it comes from, I think it might always just be there, but it only blooms when conditions are right.